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[NiFe] Hydrogenase from Desulfovibrio desulfuricans ATCC 27774
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FRV PDB ENTRY 1FRV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 25% (W/V) PEG 4000, 0.1 M TRIS-HCL BUFFER PH 8.5, 0.2 M MGCL2 AND A TRACE AMOUNT OF A DETERGENT, C12-DAO.
Crystal Properties Matthews coefficient Solvent content 2.23 44.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.09 α = 90 b = 169.98 β = 92.8 c = 72.62 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 100 CCD ADSC CCD TOROIDAL MIRROR 1999-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.8 32 95.4 0.072 4.5 2.5 135264
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 1.8 1.9 96 0.412 1.7 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1FRV 1.8 25 135233 6552 95.4 0.1671 0.1583 0.2231 RANDOM SAMPLE
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 6 11896.01 13663.51
RMS Deviations Key Refinement Restraint Deviation s_from_restr_planes 0.337 s_anti_bump_dis_restr 0.059 s_similar_dist 0.051 s_non_zero_chiral_vol 0.041 s_similar_adp_cmpnt 0.04 s_zero_chiral_vol 0.035 s_approx_iso_adps 0.03 s_angle_d 0.022 s_bond_d 0.021 s_rigid_bond_adp_cmpnt
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12352 Nucleic Acid Atoms Solvent Atoms 1399 Heterogen Atoms 74
Software Software Software Name Purpose SHELXL-97 refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing