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3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at 160 MPa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VKZ PDB ENTRY 3VKZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 PEG 3350, calcium chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.56 52.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.298 α = 90 b = 58.251 β = 119.09 c = 76.044 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD ADSC QUANTUM 210r 2011-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 0.700 Photon Factory AR-NW12A
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 2.06 50 83.2 0.049 14.5 2.2 20579
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 2.06 2.1 85.9 0.157 1.9
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 ENTRY 3VKZ 2.06 35.31 19521 1057 83.18 0.13888 0.13603 0.1367 0.19117 0.1892 RANDOM 19.355
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] 0.16 0.16 0.04 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.937 r_dihedral_angle_4_deg 18.537 r_dihedral_angle_3_deg 16.336 r_dihedral_angle_1_deg 6.313 r_scangle_it 5.678 r_scbond_it 3.58 r_mcangle_it 2.173 r_angle_refined_deg 1.89 r_mcbond_it 1.209 r_chiral_restr 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.937 r_dihedral_angle_4_deg 18.537 r_dihedral_angle_3_deg 16.336 r_dihedral_angle_1_deg 6.313 r_scangle_it 5.678 r_scbond_it 3.58 r_mcangle_it 2.173 r_angle_refined_deg 1.89 r_mcbond_it 1.209 r_chiral_restr 0.136 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2759 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 14
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SERGUI data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing