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Wild-type chorismate mutase of Bacillus subtilis at 1.6 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DBF PDB ENTRY 1DBF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 100 MM MMT BUFFER ---MALIC ACID, MES, TRIS, IN MOLAR RATIOS OF 1:2:2, RESPECTIVELY--- PH 6.0, 100 MM MAGNESIUM CHLORIDE, 25% W/V PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.12 41.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.498 α = 90 b = 165.174 β = 118.67 c = 49.586 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 IMAGE PLATE RIGAKU IMAGE PLATE 2011-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 1.59 82.58 85 0.05 14.4 2.9 93148
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 1.59 1.69 59.4 0.18 4.4 2.2
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 PDB ENTRY 1DBF 1.59 82.6 82445 4383 93.1 0.1452 0.14386 0.14 0.16975 0.168 RANDOM 14.774
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] -0.1 0.26 0.22 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.785 r_sphericity_free 17.943 r_dihedral_angle_4_deg 15.797 r_dihedral_angle_3_deg 15.135 r_rigid_bond_restr 7.959 r_dihedral_angle_1_deg 5.77 r_sphericity_bonded 5.724 r_angle_refined_deg 1.171 r_chiral_restr 0.074 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.785 r_sphericity_free 17.943 r_dihedral_angle_4_deg 15.797 r_dihedral_angle_3_deg 15.135 r_rigid_bond_restr 7.959 r_dihedral_angle_1_deg 5.77 r_sphericity_bonded 5.724 r_angle_refined_deg 1.171 r_chiral_restr 0.074 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5586 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing