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Tungsten containing Formate Dehydrogenase from Desulfovibrio Gigas
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NAP PDB ENTRY 2NAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 0.1M HEPES 7.5, 20% PEG 3350 (W/V), 10% ISOPROPANOL (V/V), 1% BETA-OCTYLGLUCOSIDE, 4 DEGREES CELCIUS, HANGING DROPS., pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.65 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.408 α = 90 b = 110.398 β = 93.53 c = 156.185 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 MARRESEARCH 1999-11-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.992,1.214,1.735,1.7415 ESRF BM14
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 35 92 0.078 5 1.9 220129
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 1.88 70 0.6 2 1.65
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2NAP 1.8 35 208782 10979 95.7 0.169 0.167 0.201 RANDOM 19.1
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] -0.43 0.38 1.22 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.862 r_dihedral_angle_1_deg 4.495 r_scangle_it 1.889 r_angle_refined_deg 1.563 r_mcangle_it 1.502 r_scbond_it 1.336 r_mcbond_it 0.97 r_symmetry_vdw_refined 0.299 r_symmetry_hbond_refined 0.244 r_nbd_refined 0.218
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.862 r_dihedral_angle_1_deg 4.495 r_scangle_it 1.889 r_angle_refined_deg 1.563 r_mcangle_it 1.502 r_scbond_it 1.336 r_mcbond_it 0.97 r_symmetry_vdw_refined 0.299 r_symmetry_hbond_refined 0.244 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.107 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18786 Nucleic Acid Atoms Solvent Atoms 1708 Heterogen Atoms 288
Software Software Software Name Purpose O model building SCALEPACK data scaling SHARP phasing AMoRE phasing ARP/wARP phasing O phasing REFMAC refinement