☰ Navigation Tabs
The crystal structure of D-lactate dehydrogenase from Escherichia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J49 PDB ENTRY 1J49
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 298 100mM sodium acetate (pH 4.5), 0.8M sodium dihydrogenphosphate, 1.2M potassium monohydrogen phosphate., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.26 62.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.029 α = 90 b = 131.029 β = 90 c = 405.746 γ = 120
Symmetry Space Group P 61 2 2
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 2012-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.3 55.03 100 32130 32128
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.48 100
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1J49 3.3 55.03 32046 30412 1631 99.95 0.23347 0.23143 0.2435 0.27116 0.2854 RANDOM 73.871
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] 0.62 0.62 0.62 -2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.939 r_dihedral_angle_3_deg 20.078 r_dihedral_angle_4_deg 17.669 r_long_range_B_refined 11.063 r_long_range_B_other 11.063 r_scangle_other 8.279 r_mcangle_it 8.002 r_mcangle_other 8.002 r_dihedral_angle_1_deg 6.955 r_mcbond_it 5.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.939 r_dihedral_angle_3_deg 20.078 r_dihedral_angle_4_deg 17.669 r_long_range_B_refined 11.063 r_long_range_B_other 11.063 r_scangle_other 8.279 r_mcangle_it 8.002 r_mcangle_other 8.002 r_dihedral_angle_1_deg 6.955 r_mcbond_it 5.146 r_scbond_it 5.144 r_mcbond_other 5.143 r_scbond_other 5.143 r_angle_refined_deg 1.422 r_angle_other_deg 1.071 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.005 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 8746 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling