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Structure of saposin B in complex with chloroquine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N69 PDB ENTRY 1N69
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.1M MES, PH 6.0, 30% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.77 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.299 α = 90 b = 75.299 β = 90 c = 94.716 γ = 120
Symmetry Space Group P 32 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 6M 2014-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.13 38 98.9 0.08 14.4 6.9 17890 1.6 43.94
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 2.13 2.2 92.5 1 1.6 6.9
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 1N69 2.13 15 17711 908 99.59 0.2303 0.229 0.2342 0.2538 0.2602 RANDOM 65.52
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] -7.2465 -7.2465 14.4929
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.85 t_omega_torsion 2.13 t_angle_deg 1.08 t_bond_d 0.009 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_other_torsion 16.85 t_omega_torsion 2.13 t_angle_deg 1.08 t_bond_d 0.009 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 1806 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 44
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling