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Carbamate kinase from Enterococcus faecalis bound to MgADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B7B PDB ENTRY 1B7B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 CRYSTALS WERE OBTAINED AT 4 DEGREES USING THE HANGING DROP VAPOUR DIFFUSION METHOD BY MIXING 1.5 MIRCROLITERS OF A 10 MG/ML PROTEIN SOLUTION IN 5 MM SODIUM CACODYLATE PH 6.5, 2 MM ADP, 5 MM MGCL2 AND 50 MM SODIUM PHOPHONOACETATE, AND 1.5 MICROLITERS OF THE RESERVOIR BUFFER CONTAINING 13-16% PEG 8000, 130-160 MM MAGNESIUM ACETATE AND 0.1 M SODIUM CACODYLATE PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.25 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.522 α = 90 b = 103.522 β = 90 c = 155.414 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 1998-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 1.39 50 90.4 0.05 7 3.3 172839 20
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 1.39 1.47 87.1 0.33 2.2 2.9
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 (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 1B7B 1.39 20 172736 8668 89.7 0.2012 0.2012 0.2063 0.2103 0.2163 RANDOM 24.7
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] -0.22 -0.683 -0.22 0.441
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.228 c_bond_d 0.004 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.228 c_bond_d 0.004 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6909 Nucleic Acid Atoms Solvent Atoms 840 Heterogen Atoms 88
Software Software Software Name Purpose CNS refinement MOSFLM data reduction SCALA data scaling AMoRE phasing