☰ Navigation Tabs
Crystal structure of glycerol phosphate phosphatase Rv1692 from Mycobacterium tuberculosis in complex with calcium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PDW PDB ENTRY 3PDW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 HEPES (50 mM) pH 7.5 PEG 4000 (10% w/v), Sodium citrate trihydrate (40 mM), and CaCl2 (100 mM), VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.18 43.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.814 α = 90 b = 70.318 β = 95.56 c = 97.099 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 MARMOSAIC 300 mm CCD 2012-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0 APS 21-ID-D
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 2.2 50 98.5 31079 30613 2
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 3PDW 2.21 40 31079 30613 1640 97.27 0.19373 0.19102 0.1933 0.24284 0.2368 RANDOM 38.093
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] 1.8 -0.26 -1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.676 r_dihedral_angle_4_deg 19.503 r_dihedral_angle_3_deg 17.584 r_dihedral_angle_1_deg 5.387 r_angle_refined_deg 1.146 r_angle_other_deg 0.765 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.676 r_dihedral_angle_4_deg 19.503 r_dihedral_angle_3_deg 17.584 r_dihedral_angle_1_deg 5.387 r_angle_refined_deg 1.146 r_angle_other_deg 0.765 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 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_scbond_it 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 4997 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 4
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling