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Crystal Structure of SafC from Myxococcus xanthus apo-Form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HNK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 PEG MME 5000, Sodium Acetate pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.71 54.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.558 α = 90 b = 64.558 β = 90 c = 118.163 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 PIXEL DECTRIS PILATUS 2M mirrors 2014-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.999990 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) 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 1.31 118.16 100 0.144 0.152 0.994 12.6 20.2 69174 13.71
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.311 1.38 100 1.274 0.405 2.3 20.3
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 2HNK 1.31 19.18 68892 3376 99.5 0.178 0.177 0.1893 0.196 0.2065 RANDOM 20.01
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] 0.0702 0.0702 -0.1404
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.15 t_omega_torsion 3.6 t_angle_deg 0.99 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_other_torsion 16.15 t_omega_torsion 3.6 t_angle_deg 0.99 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 1677 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 33
Software Software Software Name Purpose Aimless data scaling autoPROC data collection BUSTER-TNT refinement PDB_EXTRACT data extraction MOLREP phasing XDS data reduction