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E. coli Hydrogenase-1 variant P508A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A4M pdb 5a4m
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 Peg 3350,
50 mM Bis-tris,
200 mM LiSO4,
150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.28 46.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.691 α = 90 b = 98.589 β = 90 c = 185.373 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2015-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.2 98.6 100 0.13 0.995 7.3 7.2 536585
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 99.5 1.6 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb 5a4m 1.2 92.69 509698 26714 99.97 0.12171 0.12071 0.1212 0.14052 0.1411 RANDOM 15.85
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] 0.1 0.32 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.262 r_sphericity_free 23.184 r_dihedral_angle_4_deg 17.563 r_dihedral_angle_3_deg 12.099 r_sphericity_bonded 7.659 r_dihedral_angle_1_deg 6.132 r_rigid_bond_restr 5.823 r_long_range_B_refined 2.853 r_long_range_B_other 2.558 r_scangle_other 2.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.262 r_sphericity_free 23.184 r_dihedral_angle_4_deg 17.563 r_dihedral_angle_3_deg 12.099 r_sphericity_bonded 7.659 r_dihedral_angle_1_deg 6.132 r_rigid_bond_restr 5.823 r_long_range_B_refined 2.853 r_long_range_B_other 2.558 r_scangle_other 2.256 r_scbond_it 2.026 r_scbond_other 1.996 r_angle_refined_deg 1.894 r_mcangle_it 1.411 r_mcangle_other 1.411 r_angle_other_deg 1.22 r_mcbond_other 1.14 r_mcbond_it 1.139 r_chiral_restr 0.115 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 Atoms Number Protein Atoms 13242 Nucleic Acid Atoms Solvent Atoms 1371 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing