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Crystal Structure of a Putative Cystathionine beta-Synthase from Coxiella burnetii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M54 PDB ENTRY 1M54
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 20% PEG3350, 0.05 M sodium chloride, 0.1 M Tris, 2% ethylene glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.06 40.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.171 α = 90 b = 99.739 β = 90 c = 42.497 γ = 90
Symmetry Space Group P 21 21 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 MARMOSAIC 225 mm CCD Be Lens 2013-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.736 30 97.6 0.04 20.1 4.6 29333 29333 -3 29.07
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 1.736 1.78 87.2 0.654 4.1 1313
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 1M54 1.74 21.69 29333 29035 1475 96.59 0.1969 0.1969 0.1949 0.1934 0.2324 0.2294 RANDOM 39.68
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] -0.086 -1.707 1.793
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.36 t_other_torsion 2.59 t_angle_deg 1.01 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.36 t_other_torsion 2.59 t_angle_deg 1.01 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2182 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 2
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing BUSTER-TNT refinement PDB_EXTRACT data extraction BLU-MAX data collection HKL-2000 data reduction MrBump/MolRep phasing BUSTER refinement