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Crystal structure of IPMDH from the last common ancestor of Bacillus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V53 PDB ENTRY 1V53
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 200mM diammonium hydrogen citrate, 2mM MgSO4, 15% PEG 3350, 4% glycerol, pH 5.5, temperature 291K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.266 α = 90 b = 75.985 β = 90 c = 171.225 γ = 90
Symmetry Space Group P 21 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MAR scanner 345 mm plate msc osmic optics 2010-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.8 44.549 95.2 0.092 12.4 5 22393 22393
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 87.8 0.566 0.566 0.623 0.251 1.4 4.8 2953
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 1V53 2.8 44.43 22331 1124 94.46 0.2367 0.2328 0.2285 0.3088 0.3016 RANDOM 65.5073
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] 0.78 -0.05 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.704 r_dihedral_angle_4_deg 23.235 r_dihedral_angle_3_deg 22.192 r_dihedral_angle_1_deg 6.791 r_scangle_it 2.703 r_angle_refined_deg 1.55 r_scbond_it 1.506 r_mcangle_it 1.129 r_mcbond_it 0.597 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.704 r_dihedral_angle_4_deg 23.235 r_dihedral_angle_3_deg 22.192 r_dihedral_angle_1_deg 6.791 r_scangle_it 2.703 r_angle_refined_deg 1.55 r_scbond_it 1.506 r_mcangle_it 1.129 r_mcbond_it 0.597 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5212 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction