8RKP

Cytochrome c prime from Hydrogenophilus thermoluteolus: Ferrous recombinant native with bound NO


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5B3INative state

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52930.1 M sodium acetate pH 4.5, 0.2 M lithium sulphate, 30% (w/v) PEG 8,000 in a 96-well in-situ plate
Crystal Properties
Matthews coefficientSolvent content
2.9358.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.671α = 90
b = 83.671β = 90
c = 88.247γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2022-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6372.571000.1170.120.0270.99913.419.723390
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.631.6699.94.2554.3620.9520.30.420.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6372.5722222113199.970.198350.197270.21928RANDOM33.946
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]
0.030.010.03-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.735
r_dihedral_angle_4_deg18.175
r_dihedral_angle_3_deg14.96
r_long_range_B_refined9.397
r_long_range_B_other9.345
r_scangle_other7.969
r_scbond_it5.566
r_scbond_other5.565
r_dihedral_angle_1_deg5.184
r_mcangle_it4.211
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.735
r_dihedral_angle_4_deg18.175
r_dihedral_angle_3_deg14.96
r_long_range_B_refined9.397
r_long_range_B_other9.345
r_scangle_other7.969
r_scbond_it5.566
r_scbond_other5.565
r_dihedral_angle_1_deg5.184
r_mcangle_it4.211
r_mcangle_other4.208
r_mcbond_other2.89
r_mcbond_it2.889
r_angle_refined_deg2.431
r_angle_other_deg1.578
r_chiral_restr0.307
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_gen_planes_other0.003
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1029
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms81

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
xia2data scaling
PHASERphasing