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Fic protein from Neisseria meningitidis (NmFic) mutant E156R Y183F in dimeric form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CKL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.8 277.15 10 mM Tris pH 7.8, 100 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.74 54.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.375 α = 90 b = 50.697 β = 90 c = 129.778 γ = 90
Symmetry Space Group P 2 21 21
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 2013-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.8000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 0.99 47.22 96.8 0.04 0.017 0.999 23.4 6.4 126436
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.99 1.01 89.6 0.6 0.254 0.783 3 6.4 5729
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 5CKL 0.99 47.22 120051 6297 96.6 0.1354 0.1343 0.1433 0.1553 0.1634 RANDOM 11.055
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] -0.3 0.42 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.959 r_sphericity_free 25.102 r_dihedral_angle_4_deg 13.356 r_dihedral_angle_3_deg 12.848 r_sphericity_bonded 9.717 r_rigid_bond_restr 6.322 r_dihedral_angle_1_deg 5.548 r_angle_refined_deg 2.088 r_mcangle_it 1.659 r_mcbond_it 1.458
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.959 r_sphericity_free 25.102 r_dihedral_angle_4_deg 13.356 r_dihedral_angle_3_deg 12.848 r_sphericity_bonded 9.717 r_rigid_bond_restr 6.322 r_dihedral_angle_1_deg 5.548 r_angle_refined_deg 2.088 r_mcangle_it 1.659 r_mcbond_it 1.458 r_mcbond_other 1.227 r_angle_other_deg 1.053 r_chiral_restr 0.119 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1488 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction