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Three-dimensional Structure of The Carbon Monoxide Complex of [NiFe]hydrogenase From Desulufovibrio vulgaris Miyazaki F
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H2R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 283 MPD, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2 34.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.81 α = 90 b = 125.5 β = 90 c = 66.59 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 CCD MARRESEARCH 2000-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 0.700 SPring-8 BL44B2
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 1.12 25.1 94.3 0.08 303804 297600 1 2
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) 1.12 1.18 84.9 0.384
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1H2R 1.2 20 1 244116 189902 16936 89.1 0.1259 0.1198 0.1172 0.1611 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 298 7100.31
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.093 s_non_zero_chiral_vol 0.091 s_zero_chiral_vol 0.08 s_angle_d 0.071 s_similar_adp_cmpnt 0.051 s_anti_bump_dis_restr 0.038 s_from_restr_planes 0.0286 s_bond_d 0.015 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6196 Nucleic Acid Atoms Solvent Atoms 886 Heterogen Atoms 34
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling CNS refinement SHELXL-97 refinement CCP4 data scaling CNS phasing