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Crystal structure of Lactate/malate dehydrogenase from Brucella melitensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SOW pdb entry 1sow, modified with ccp4 program chainsaw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 JCSG+ SCREEN, D12: 40MM K-PO4, 16% PEG 8000, 20% GLYCEROL, BRABA.00005.A AT 28.5MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.86 57.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.75 α = 90 b = 114.35 β = 90 c = 148.57 γ = 90
Symmetry Space Group P 21 21 21
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 210 2009-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
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 2.3 90.62 99.8 0.097 16.9 6.3 70152 69983 -3 35.96
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) 2.3 2.36 99.8 0.61 2.1 3.8 5116
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR THROUGHOUT pdb entry 1sow, modified with ccp4 program chainsaw 2.3 90 69915 69915 3526 99.8 0.176 0.174 0.1717 0.218 0.2156 RANDOM 20.79
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] 1.3 -0.47 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.737 r_dihedral_angle_4_deg 18.209 r_dihedral_angle_3_deg 15.034 r_dihedral_angle_1_deg 5.643 r_scangle_it 4.069 r_scbond_it 2.573 r_mcangle_it 1.615 r_angle_refined_deg 1.585 r_angle_other_deg 0.949 r_mcbond_it 0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.737 r_dihedral_angle_4_deg 18.209 r_dihedral_angle_3_deg 15.034 r_dihedral_angle_1_deg 5.643 r_scangle_it 4.069 r_scbond_it 2.573 r_mcangle_it 1.615 r_angle_refined_deg 1.585 r_angle_other_deg 0.949 r_mcbond_it 0.85 r_mcbond_other 0.18 r_chiral_restr 0.091 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9224 Nucleic Acid Atoms Solvent Atoms 620 Heterogen Atoms 176
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling