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2.9A resolution structure of SRPN2 (K198C/E359C) from Anopheles gambiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PZF PDB ENTRY 3PZF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.9 293 1.0 M sodium phosphate monobasic monohydrate, potassium phosphate dibasic, pH 6.9, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.76 55.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.925 α = 90 b = 164.392 β = 90.02 c = 186.181 γ = 90
Symmetry Space Group P 1 21 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 2014-10-18 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-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 2.9 47.82 99.5 0.135 7.9 3.4 129666 129666 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.95 99.8 0.635 0.418 2 3.3 6417
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 3PZF 2.9 47.82 -3 129619 6285 99.34 0.1968 0.1939 0.1962 0.2545 0.2549 RANDOM 42.018
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] -32.69 0.23 67.51 -34.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.441 r_dihedral_angle_3_deg 16.113 r_dihedral_angle_4_deg 14.732 r_dihedral_angle_1_deg 6.208 r_mcangle_it 2.81 r_mcbond_it 1.619 r_mcbond_other 1.619 r_angle_refined_deg 1.08 r_angle_other_deg 0.71 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.441 r_dihedral_angle_3_deg 16.113 r_dihedral_angle_4_deg 14.732 r_dihedral_angle_1_deg 6.208 r_mcangle_it 2.81 r_mcbond_it 1.619 r_mcbond_other 1.619 r_angle_refined_deg 1.08 r_angle_other_deg 0.71 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33765 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction JDirector data collection XDS data reduction