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Crystal structure of1-pyrroline-4-hydroxy-2-carboxylate deaminase from Brucella melitensis ATCC 23457
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HMC pdb entry 2hmc
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 EmeraldBio MCSG1 screen, a11: 10% PEG 4000, 200mM MgCl2, 100mM MES/NaOH pH 6.5; cryo 20% EG; BrmeB.01563.a.B1.PS01874 at 19.3mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.29 46.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.06 α = 90 b = 95.06 β = 90 c = 125.33 γ = 120
Symmetry Space Group P 63 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 RIGAKU SATURN 944+ RIGAKU VARIMAX 2013-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.75 50 99.7 0.057 22.33 6.9 34409 34293 -3 25.711
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 1.75 1.8 98.3 0.485 3.13
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 pdb entry 2hmc 1.75 44.48 34409 34269 1732 99.69 0.1599 0.1599 0.1586 0.1703 0.1846 0.1898 RANDOM 20.2893
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] 0.15 0.15 0.15 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.709 r_dihedral_angle_4_deg 14.74 r_dihedral_angle_3_deg 11.52 r_dihedral_angle_1_deg 6.039 r_mcangle_it 1.586 r_angle_refined_deg 1.472 r_mcbond_it 0.986 r_mcbond_other 0.972 r_angle_other_deg 0.819 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.709 r_dihedral_angle_4_deg 14.74 r_dihedral_angle_3_deg 11.52 r_dihedral_angle_1_deg 6.039 r_mcangle_it 1.586 r_angle_refined_deg 1.472 r_mcbond_it 0.986 r_mcbond_other 0.972 r_angle_other_deg 0.819 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2432 Nucleic Acid Atoms Solvent Atoms 391 Heterogen Atoms 4
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction JDirector data collection XDS data reduction