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Re-refined structure of R-state L-lactate dehydrogenase fromLactobacillus casei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZQZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 298 ammonium sulfate, sodium citrate, potassium sodium tartrate
Crystal Properties Matthews coefficient Solvent content 2.93 58.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.382 α = 90 b = 82.893 β = 91.21 c = 179.771 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 ADSC QUANTUM 4 2000-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.978 Photon Factory BL-6A
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 2.1 34.1 99.9 0.065 7.1 2.6 168255 36.9
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 2.1 2.21 93.3 0.509 0.9 1.9
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 2ZQZ 2.3 34.1 102055 5411 99.9 0.19535 0.19396 0.2005 0.22166 0.2271 RANDOM 48.718
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] -0.93 0.48 0.83 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.293 r_dihedral_angle_4_deg 23.715 r_dihedral_angle_3_deg 15.729 r_dihedral_angle_1_deg 6.472 r_long_range_B_refined 5.072 r_long_range_B_other 5.066 r_scangle_other 3.927 r_mcangle_it 2.902 r_mcangle_other 2.902 r_scbond_it 2.543
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.293 r_dihedral_angle_4_deg 23.715 r_dihedral_angle_3_deg 15.729 r_dihedral_angle_1_deg 6.472 r_long_range_B_refined 5.072 r_long_range_B_other 5.066 r_scangle_other 3.927 r_mcangle_it 2.902 r_mcangle_other 2.902 r_scbond_it 2.543 r_scbond_other 2.541 r_mcbond_it 1.952 r_mcbond_other 1.95 r_angle_refined_deg 1.747 r_angle_other_deg 1.429 r_chiral_restr 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14212 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing