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CRYSTAL STRUCTURE OF L-lactate dehydrogenase from Bacillus cereus ATCC 14579 complexed with calcium, NYSGRC Target 029452
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LMR PDB ENTRY 4LMR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.2M Ca-acetate, 0.1M sodium cacodylate:HCl, pH 6.5,
40% PEG300, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.09 41.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.719 α = 90 b = 75.453 β = 89.99 c = 100.145 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 315 2013-04-12 SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9791 NSLS X29A
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 1.9 50 95.4 0.064 10.8 2 184605
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 1.9 1.93 95.4 0.426 2 9175
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 4LMR 1.9 42.98 97912 4923 99.62 0.2103 0.2087 0.2073 0.241 0.2308 RANDOM 41.8931
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] -26.69 7.53 46.2 -19.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.281 r_dihedral_angle_4_deg 18.695 r_dihedral_angle_3_deg 15.763 r_dihedral_angle_1_deg 5.854 r_mcangle_it 1.887 r_scbond_it 1.371 r_angle_refined_deg 1.244 r_mcbond_it 1.109 r_chiral_restr 0.087 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.281 r_dihedral_angle_4_deg 18.695 r_dihedral_angle_3_deg 15.763 r_dihedral_angle_1_deg 5.854 r_mcangle_it 1.887 r_scbond_it 1.371 r_angle_refined_deg 1.244 r_mcbond_it 1.109 r_chiral_restr 0.087 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9936 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 6
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction