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3.0 A Model of Iron Containing Urease UreA2B2 from Helicobacter mustelae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EJX PDB ENTRY 1EJX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 6.7 mg/ml protein, 6.7 mM Tris, 20% MPD, 0.07 M sodium acetate, 0.013 M calcium chloride, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.54 65.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.98 α = 90 b = 223.94 β = 90 c = 395.87 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 315r 2010-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.998 67.292 98.6 0.201 0.201 9.3 8.8 145678 145678 -3 59.84
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.16 94.3 0.809 0.809 0.9 5.1 20140
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 1EJX 3 67.29 145355 145355 7283 0.1711 0.1711 0.1701 0.1768 0.1894 0.1936 RANDOM 32.168
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] 0.6073 -1.9346 1.3273
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.38 t_omega_torsion 2.75 t_angle_deg 1.17 t_improper_torsion 1.007 t_gen_planes 0.0144 t_bond_d 0.0089 t_trig_c_planes 0.0073 t_dihedral_angle_d t_it t_nbd
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.38 t_omega_torsion 2.75 t_angle_deg 1.17 t_improper_torsion 1.007 t_gen_planes 0.0144 t_bond_d 0.0089 t_trig_c_planes 0.0073 t_dihedral_angle_d t_it t_nbd t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 36408 Nucleic Acid Atoms Solvent Atoms 606 Heterogen Atoms 12
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing BUSTER-TNT refinement PDB_EXTRACT data extraction BOS data collection BUSTER refinement