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3-isopropylmalate dehydrogenase from Shewanella benthica DB21 MT-2
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 6.7 293 PEG 3350, sodium chloride, HEPES, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.972 α = 90 b = 59.208 β = 95.12 c = 119.779 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 QUANTUM 270 2010-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.000 Photon Factory AR-NE3A
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 1.48 50 98.1 0.04 19.3 3.6 118167
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 1.48 1.51 96.1 0.322 3.2 5710
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3VKZ 1.48 25.77 118063 5928 97.95 0.1953 0.1934 0.2319 0.231 RANDOM 19.8483
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] -0.76 -0.36 1.01 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.137 r_dihedral_angle_4_deg 19.01 r_dihedral_angle_3_deg 13.011 r_dihedral_angle_1_deg 6.147 r_scangle_it 5.013 r_scbond_it 3.326 r_angle_refined_deg 2.446 r_mcangle_it 2.261 r_mcbond_it 1.534 r_chiral_restr 0.177
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.137 r_dihedral_angle_4_deg 19.01 r_dihedral_angle_3_deg 13.011 r_dihedral_angle_1_deg 6.147 r_scangle_it 5.013 r_scbond_it 3.326 r_angle_refined_deg 2.446 r_mcangle_it 2.261 r_mcbond_it 1.534 r_chiral_restr 0.177 r_bond_refined_d 0.029 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5594 Nucleic Acid Atoms Solvent Atoms 709 Heterogen Atoms 28
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