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Crystal structure of putative 5-enolpyruvoylshikimate-3-phosphate synthase from Bacillus halodurans C-125
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RF4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 2.0 M amm. sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.08 60.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.856 α = 90 b = 140.748 β = 90 c = 193.625 γ = 90
Symmetry Space Group P 21 21 21
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 315 2010-11-30 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9791 NSLS X29A
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 2.8 50 99.7 0.105 6.4 7.1 59796
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.85 96.5 6.6
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 1RF4 2.8 20 56315 2998 99.37 0.22551 0.22232 0.2215 0.28626 0.2815 RANDOM 74.057
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] 0.09 -0.01 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.819 r_dihedral_angle_3_deg 19.855 r_dihedral_angle_4_deg 14.101 r_scbond_it 8.841 r_dihedral_angle_1_deg 5.58 r_mcangle_it 3.584 r_angle_refined_deg 1.207 r_mcbond_it 0.58 r_scangle_it 0.428 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.819 r_dihedral_angle_3_deg 19.855 r_dihedral_angle_4_deg 14.101 r_scbond_it 8.841 r_dihedral_angle_1_deg 5.58 r_mcangle_it 3.584 r_angle_refined_deg 1.207 r_mcbond_it 0.58 r_scangle_it 0.428 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12789 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 145
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction