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Membrane-bound respiratory [NiFe] hydrogenase from Hydrogenovibrio marinus in an air-oxidized condition
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AYX PDB ENTRY 3AYX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M PIPES, 15% PEG 3350, 300mM lithium sulfate, 5mM DTT, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.56 51.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.646 α = 90 b = 116.664 β = 91.34 c = 113.612 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD RAYONIX MX225HE 2010-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.22 20 99.6 0.084 12.5 4.1 582417 578159 10.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.22 1.24 99.4 0.385 3.3 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FREE R PDB ENTRY 3AYX 1.22 20 1035058 1035058 54353 100 0.139 0.139 0.1279 0.171 0.1494 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 52 13111 15255.7
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.117 s_non_zero_chiral_vol 0.103 s_zero_chiral_vol 0.102 s_anti_bump_dis_restr 0.073 s_similar_adp_cmpnt 0.054 s_angle_d 0.034 s_from_restr_planes 0.0311 s_bond_d 0.018 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13529 Nucleic Acid Atoms Solvent Atoms 1631 Heterogen Atoms 110
Software Software Software Name Purpose BSS data collection MOLREP phasing SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling