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CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHONOPYRUVATE HYDROLASE (MLL9387) FROM MESORHIZOBIUM LOTI MAFF303099 AT 2.15 A RESOLUTION
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 277 NANODROP, 3.0% PEG 4000, 23.3% Glycerol, 0.1M Sodium acetate pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 4.00
Crystal Properties Matthews coefficient Solvent content 3.1 60.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.269 α = 90 b = 180.269 β = 90 c = 185.514 γ = 120
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 1M LONG RH COATED BENT CYLINDRICAL MIRROR FOR HORIZONTAL AND VERTICAL FOCUSING 2007-01-29 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL1-5 0.918381, 0.979354 SSRL BL1-5
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 2.15 45.083 99.3 0.093 8.34 3.31 121425 37.31
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 2.15 2.23 99.6 0.764 1.6 3.28
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.15 45.08 121409 6092 99.3 0.165 0.162 0.172 0.204 0.2101 RANDOM 43.89
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] 0.13 0.07 0.13 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.708 r_dihedral_angle_4_deg 15.376 r_dihedral_angle_3_deg 15.134 r_scangle_it 6.594 r_dihedral_angle_1_deg 5.556 r_scbond_it 4.789 r_mcangle_it 2.283 r_mcbond_it 1.404 r_angle_refined_deg 1.249 r_angle_other_deg 0.888
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.708 r_dihedral_angle_4_deg 15.376 r_dihedral_angle_3_deg 15.134 r_scangle_it 6.594 r_dihedral_angle_1_deg 5.556 r_scbond_it 4.789 r_mcangle_it 2.283 r_mcbond_it 1.404 r_angle_refined_deg 1.249 r_angle_other_deg 0.888 r_mcbond_other 0.468 r_symmetry_vdw_other 0.274 r_nbd_refined 0.205 r_nbd_other 0.189 r_symmetry_vdw_refined 0.179 r_symmetry_hbond_refined 0.174 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.14 r_xyhbond_nbd_other 0.118 r_nbtor_other 0.086 r_chiral_restr 0.067 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12016 Nucleic Acid Atoms Solvent Atoms 712 Heterogen Atoms 82
Software Software Software Name Purpose MolProbity model building SHELX phasing REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHELXD phasing autoSHARP phasing