Experiment: 2B4M

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B4L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.25	274	Tris, ammonium acetate, PEG 4000, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 274K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.562	α = 90
b = 28.318	β = 93.87
c = 102.826	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.05	MPG/DESY, HAMBURG	BW6

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.8	15	83			13067	10846		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.84	70.7		0.312	2.4		369

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2B4L	2.8	15	13067	10300	546	82.4	0.23322	0.23056	0.28302	RANDOM	15.618

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]
-0.27		5.49	-1.16		2.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.522
r_dihedral_angle_3_deg	19.143
r_dihedral_angle_4_deg	9.138
r_dihedral_angle_1_deg	5.759
r_angle_refined_deg	1.133
r_scangle_it	0.919
r_scbond_it	0.549
r_mcangle_it	0.378
r_symmetry_vdw_refined	0.24
r_mcbond_it	0.226

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.522
r_dihedral_angle_3_deg	19.143
r_dihedral_angle_4_deg	9.138
r_dihedral_angle_1_deg	5.759
r_angle_refined_deg	1.133
r_scangle_it	0.919
r_scbond_it	0.549
r_mcangle_it	0.378
r_symmetry_vdw_refined	0.24
r_mcbond_it	0.226
r_nbd_refined	0.197
r_symmetry_hbond_refined	0.185
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4122
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

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.