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rat LDHA in complex with 2-(4-bromophenoxy)propanedioic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other INTERNAL RAT LDHA STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 1.5 M NA MALONATE PH 7.0, 2% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.298 α = 90 b = 82.51 β = 96.19 c = 129.113 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 RIGAKU SATURN 944 VARIMAXHF 2009-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E
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 2.35 30.87 99.8 0.09 8.3 3.44 54228 2
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 2.35 2.43 99.6 0.3 2.7 3.48
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 INTERNAL RAT LDHA STRUCTURE 2.35 28.99 51074 2732 98.95 0.20544 0.20197 0.2007 0.2718 0.2676 RANDOM 26.278
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 -0.14 0.14 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.549 r_dihedral_angle_4_deg 18.395 r_dihedral_angle_3_deg 15.275 r_dihedral_angle_1_deg 6.596 r_angle_refined_deg 1.483 r_angle_other_deg 0.951 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.549 r_dihedral_angle_4_deg 18.395 r_dihedral_angle_3_deg 15.275 r_dihedral_angle_1_deg 6.596 r_angle_refined_deg 1.483 r_angle_other_deg 0.951 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9970 Nucleic Acid Atoms Solvent Atoms 705 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling AMoRE phasing