Experiment: 5IIH

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3V08

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	289	1 ul of 30 mg/ml protein in 10 mM Tris pH 7.5 and 150 mM NaCl buffer was mixed with 1 ul of the well condition (0.2 M Li2SO4, 0.1 M Tris:HCl pH 7.4, 2.0 M (NH4)2SO4, 5 mM ZnCl2) and equilibrated against well solution in 15 Well Crystallization Plate (Qiagen)

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.098	α = 90
b = 93.098	β = 90
c = 141.442	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Beryllium Lenses	2014-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.979	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.4	50.01	99.6	0.071	0.071	9.3	7.7		27051		-3	56.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.44	99.3		0.965		7.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3V08	2.4	50.01	25677	1348	99.65	0.1777	0.1748	0.2354	RANDOM	72.017

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
2.39	1.19		2.39		-7.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.954
r_dihedral_angle_4_deg	19.732
r_dihedral_angle_3_deg	14.713
r_mcangle_it	8.463
r_mcbond_it	7.113
r_mcbond_other	7.113
r_dihedral_angle_1_deg	5.154
r_angle_refined_deg	1.222
r_angle_other_deg	0.918
r_chiral_restr	0.066

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.954
r_dihedral_angle_4_deg	19.732
r_dihedral_angle_3_deg	14.713
r_mcangle_it	8.463
r_mcbond_it	7.113
r_mcbond_other	7.113
r_dihedral_angle_1_deg	5.154
r_angle_refined_deg	1.222
r_angle_other_deg	0.918
r_chiral_restr	0.066
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4501
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	6

Software

Software
Software Name	Purpose
MD2	data collection
SCALEPACK	data scaling
HKL-3000	data reduction
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.