5JRD

E. coli Hydrogenase-1 variant P508A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A4Mpdb 5a4m

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6293Peg 3350, 50 mM Bis-tris, 200 mM LiSO4, 150 mM NaCl
Crystal Properties
Matthews coefficientSolvent content
2.2846.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.691α = 90
b = 98.589β = 90
c = 185.373γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.298.61000.130.9957.37.2536585
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2299.51.67

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTpdb 5a4m1.292.695096982671499.970.121710.120710.14052RANDOM15.85
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]
0.10.32-0.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.262
r_sphericity_free23.184
r_dihedral_angle_4_deg17.563
r_dihedral_angle_3_deg12.099
r_sphericity_bonded7.659
r_dihedral_angle_1_deg6.132
r_rigid_bond_restr5.823
r_long_range_B_refined2.853
r_long_range_B_other2.558
r_scangle_other2.256
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.262
r_sphericity_free23.184
r_dihedral_angle_4_deg17.563
r_dihedral_angle_3_deg12.099
r_sphericity_bonded7.659
r_dihedral_angle_1_deg6.132
r_rigid_bond_restr5.823
r_long_range_B_refined2.853
r_long_range_B_other2.558
r_scangle_other2.256
r_scbond_it2.026
r_scbond_other1.996
r_angle_refined_deg1.894
r_mcangle_it1.411
r_mcangle_other1.411
r_angle_other_deg1.22
r_mcbond_other1.14
r_mcbond_it1.139
r_chiral_restr0.115
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.002
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13242
Nucleic Acid Atoms
Solvent Atoms1371
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing