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Crystal structure of Phosphoribosylaminoimidazole carboxylase catalytic subunit from Burkholderia cenocepacia J2315
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 289 EBS INTERNAL TRACKING NUMBER HEPES (PH 7.0), 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 UL X 0.4 UL DROP WITH 0.1 M BICINE (PH 9.0), 10% (V/V) MPD. 20% ETHYLENE GLYCOL CRYOPROTECTANT, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
Crystal Properties Matthews coefficient Solvent content 2.88 57.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.51 α = 90 b = 117.18 β = 90 c = 122.31 γ = 90
Symmetry Space Group I 2 2 2
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 2012-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.977408 ALS 5.0.1
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 1.85 100 0.089 16.28 71473 -3 22.7
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 1.85 1.9 100 0.51 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 MOLECULAR REPLACEMENT THROUGHOUT 1XMP 1.85 48.122 71471 3618 0.148 0.147 0.1537 0.176 0.1814 RANDOM 12.97
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] -0.29 -0.4 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.679 r_dihedral_angle_4_deg 21.028 r_dihedral_angle_3_deg 12.357 r_dihedral_angle_1_deg 5.6 r_angle_refined_deg 1.351 r_angle_other_deg 0.944 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.679 r_dihedral_angle_4_deg 21.028 r_dihedral_angle_3_deg 12.357 r_dihedral_angle_1_deg 5.6 r_angle_refined_deg 1.351 r_angle_other_deg 0.944 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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 4908 Nucleic Acid Atoms Solvent Atoms 672 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement