5LMM

Structure of E coli Hydrogenase Hyd-1 mutant E28Q


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A4Ipdb 5a4i

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293100 mM tris pH 8.1 150 mM NaCl 200 mM LiSO4 20-24% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.1141.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.981α = 90
b = 97.799β = 90
c = 183.474γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6Mmirrors2016-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.291.7497.90.140.9989.110.9511277
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.2295.61.9640.5941.310.4

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 5a4i1.291.744850822598797.720.118930.117520.14561RANDOM14.04
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]
0.170.14-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.901
r_sphericity_free21.839
r_dihedral_angle_4_deg16.87
r_dihedral_angle_3_deg11.507
r_sphericity_bonded7.433
r_dihedral_angle_1_deg6.023
r_long_range_B_refined2.867
r_long_range_B_other2.867
r_rigid_bond_restr2.765
r_scangle_other2.755
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.901
r_sphericity_free21.839
r_dihedral_angle_4_deg16.87
r_dihedral_angle_3_deg11.507
r_sphericity_bonded7.433
r_dihedral_angle_1_deg6.023
r_long_range_B_refined2.867
r_long_range_B_other2.867
r_rigid_bond_restr2.765
r_scangle_other2.755
r_scbond_it2.407
r_scbond_other2.407
r_angle_refined_deg1.785
r_mcangle_it1.43
r_mcangle_other1.43
r_mcbond_it1.212
r_mcbond_other1.212
r_angle_other_deg1.112
r_chiral_restr0.123
r_bond_refined_d0.017
r_gen_planes_refined0.011
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13167
Nucleic Acid Atoms
Solvent Atoms1426
Heterogen Atoms123

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing