6GAM

Structure of E14Q variant of E. coli hydrogenase-2 (as-isolated enzyme)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6EQH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.9296100 mM Bis-tris pH 5.9 200 mM MgCl2 18-22% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1541.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.477α = 90
b = 100.471β = 90
c = 168.656γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-07-23MSINGLE 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)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
11.41681000.1049.47.2330441
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.421001.177.2

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 REPLACEMENTTHROUGHOUT6EQH1.486.32313703165771000.1510.150.17RANDOM15.61
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]
0.450.07-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.907
r_dihedral_angle_4_deg19.174
r_dihedral_angle_3_deg11.62
r_dihedral_angle_1_deg6.099
r_long_range_B_refined3.823
r_long_range_B_other3.757
r_scangle_other2.978
r_scbond_other1.936
r_scbond_it1.935
r_angle_refined_deg1.709
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.907
r_dihedral_angle_4_deg19.174
r_dihedral_angle_3_deg11.62
r_dihedral_angle_1_deg6.099
r_long_range_B_refined3.823
r_long_range_B_other3.757
r_scangle_other2.978
r_scbond_other1.936
r_scbond_it1.935
r_angle_refined_deg1.709
r_mcangle_it1.6
r_mcangle_other1.6
r_mcbond_it1.119
r_mcbond_other1.119
r_angle_other_deg1.04
r_chiral_restr0.107
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12645
Nucleic Acid Atoms
Solvent Atoms1068
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing