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carboxymethylproline synthase (CarB) from pectobacterium carotovora, complexed with acetyl CoA and bicine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A7K monomer of 2A7K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 PEG 6000, BICINE, pH 8, vapor diffusion, hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.7 53.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.605 α = 90 b = 139.605 β = 90 c = 78.546 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 MARMOSAIC 225 mm CCD mirrors 2005-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 1.009 SRS PX10.1
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 3.15 47.91 99.3 0.203 5.9 15149
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 3.15 3.26 94.3 0.562 3.9
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 (All) 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 monomer of 2A7K 3.15 47.91 15136 798 99.23 0.194 0.194 0.192 0.1981 0.232 0.2313 RANDOM 45.538
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] 0.75 0.38 0.75 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.448 r_dihedral_angle_4_deg 17.216 r_dihedral_angle_3_deg 16.913 r_dihedral_angle_1_deg 5.498 r_angle_refined_deg 1.114 r_scangle_it 0.903 r_angle_other_deg 0.747 r_scbond_it 0.505 r_mcangle_it 0.307 r_symmetry_hbond_refined 0.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.448 r_dihedral_angle_4_deg 17.216 r_dihedral_angle_3_deg 16.913 r_dihedral_angle_1_deg 5.498 r_angle_refined_deg 1.114 r_scangle_it 0.903 r_angle_other_deg 0.747 r_scbond_it 0.505 r_mcangle_it 0.307 r_symmetry_hbond_refined 0.285 r_symmetry_vdw_refined 0.256 r_nbd_refined 0.225 r_symmetry_vdw_other 0.216 r_mcbond_it 0.182 r_nbtor_refined 0.18 r_nbd_other 0.17 r_xyhbond_nbd_refined 0.152 r_nbtor_other 0.087 r_chiral_restr 0.059 r_mcbond_other 0.042 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5304 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 52
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction