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Crystal structure of putative aminomethyltransferase from Leptospirillum rubarum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.9 296 0.5 M K3PO4/0.5 M Na3PO4, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 3.14 60.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.616 α = 90 b = 115.616 β = 90 c = 75.428 γ = 90
Symmetry Space Group P 43 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 ADSC QUANTUM 315r MIRRORS 2010-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 2 50 98.3 0.099 23.5 11.8 34441 -3 36.98
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 2 2.03 94.4 0.673 3 5.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 2 36.56 34384 34384 1393 98 0.185 0.184 0.184 0.214 0.2076 RANDOM 44.34
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] 1.884 1.884 -3.768
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 5.08 t_other_torsion 2.98 t_angle_deg 1.17 t_bond_d 0.013 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 5.08 t_other_torsion 2.98 t_angle_deg 1.17 t_bond_d 0.013 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 2676 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 4
Software Software Software Name Purpose SBC-Collect data collection SHELX model building MLPHARE phasing DM model building ARP/wARP model building Coot model building BUSTER refinement HKL-3000 data reduction HKL-3000 data scaling SHELX phasing DM phasing