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The apo-structure of D-lactate dehydrogenase from Fusobacterium nucleatum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J49
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 100 mM MES-Na (pH 6.0) and 1.26 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 4.86 74.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.29 α = 90 b = 116.29 β = 90 c = 234.4 γ = 90
Symmetry Space Group P 43 21 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 1.00000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 37.03 100 0.171 0.046 0.996 9.7 14.5 94385
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 100 0.831 0.229 0.908 3.2 13.7
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 1J49 2.1 37.03 89290 4714 99.64 0.18793 0.18643 0.198 0.21665 0.2271 RANDOM 31.673
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] 0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.94 r_dihedral_angle_4_deg 26.624 r_dihedral_angle_3_deg 15.198 r_long_range_B_refined 7.663 r_long_range_B_other 7.662 r_dihedral_angle_1_deg 6.395 r_scangle_other 6.235 r_scbond_it 4.122 r_scbond_other 4.122 r_mcangle_it 3.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.94 r_dihedral_angle_4_deg 26.624 r_dihedral_angle_3_deg 15.198 r_long_range_B_refined 7.663 r_long_range_B_other 7.662 r_dihedral_angle_1_deg 6.395 r_scangle_other 6.235 r_scbond_it 4.122 r_scbond_other 4.122 r_mcangle_it 3.35 r_mcangle_other 3.35 r_mcbond_it 2.399 r_mcbond_other 2.397 r_angle_refined_deg 2.102 r_angle_other_deg 1.375 r_chiral_restr 0.138 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 r_bond_other_d 0.007 r_gen_planes_other 0.006 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 5281 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement ADSC data collection SCALA data scaling ARP/wARP model building MOLREP phasing iMOSFLM data reduction