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Crystal structure of the apo form of E.Coli malate dehydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IE3 PDB ENTRY 1IE3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 20% (W/V) PEG 10000, 100 mM SODIUM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.47 50.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.466 α = 90 b = 52.485 β = 102.28 c = 170.2 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 100 CCD MARMOSAIC 225 mm CCD double crystal Si(III) monochromator with horizontal saggital focusing system, Rh coated mirror for vertical focusing 2007-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 1.283 SRS PX10.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 50 97.6 0.121 0.121 4.6 3.5 63286 63286 26.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 92.5 0.411 0.411 1.5 3.2 8651
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1IE3 2.2 50 63286 63286 3211 97.6 0.201 0.201 0.199 0.1954 0.246 0.2397 RANDOM 20.223
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] -1.69 0.04 0.71 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.502 r_dihedral_angle_4_deg 18.967 r_dihedral_angle_3_deg 16.309 r_dihedral_angle_1_deg 5.92 r_scangle_it 3.451 r_scbond_it 2.162 r_angle_refined_deg 1.493 r_mcangle_it 1.287 r_mcbond_it 0.782 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.502 r_dihedral_angle_4_deg 18.967 r_dihedral_angle_3_deg 16.309 r_dihedral_angle_1_deg 5.92 r_scangle_it 3.451 r_scbond_it 2.162 r_angle_refined_deg 1.493 r_mcangle_it 1.287 r_mcbond_it 0.782 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.182 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9060 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction MOLREP phasing