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CRYSTAL STRUCTURE OF mandelate racemase/muconate lactonizing protein from Herpetosiphon aurantiacus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JPM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 150MM POTASSIUM BROMIDE, PH 7.5, 30% PEG2000 MME, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.06 40.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.026 α = 90 b = 93.344 β = 112.6 c = 85.914 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 90 CCD ADSC QUANTUM 315 MIRRORS 2009-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.07 50 98.9 0.063 7.9 4.1 75228 -5 43.053
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 2.07 2.14 91.2 0.78 0.9 3.7
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 MR THROUGHOUT 1JPM 2.1 20 68809 2147 99.37 0.21855 0.21676 0.2167 0.27531 0.2738 RANDOM 41.917
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] -2.51 -1.49 -1.73 3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.668 r_dihedral_angle_4_deg 19.369 r_dihedral_angle_3_deg 18.049 r_scangle_it 12.844 r_scbond_it 10.315 r_mcangle_it 7.058 r_dihedral_angle_1_deg 5.467 r_mcbond_it 5.364 r_angle_refined_deg 1.253 r_nbtor_refined 0.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.668 r_dihedral_angle_4_deg 19.369 r_dihedral_angle_3_deg 18.049 r_scangle_it 12.844 r_scbond_it 10.315 r_mcangle_it 7.058 r_dihedral_angle_1_deg 5.467 r_mcbond_it 5.364 r_angle_refined_deg 1.253 r_nbtor_refined 0.291 r_xyhbond_nbd_refined 0.159 r_nbd_refined 0.146 r_symmetry_hbond_refined 0.138 r_symmetry_vdw_refined 0.119 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10201 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 16
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling