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Crystal structure of the C1QTNF5 globular domain in space group P63
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F3J PDB entry 4F3J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 2 M ammonium sulfate, 0.1 M sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.01 38.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.603 α = 90 b = 50.603 β = 90 c = 268.531 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS PILATUS 2012-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
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 1.42 134.27 99.1 0.041 30.3 8.2 72461 72440 1 3
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 1.42 1.5 93.8 0.122 8.4 3.9 10017
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4F3J 1.42 134.265 72440 68699 3645 99.03 0.10622 0.10438 0.1142 0.14168 0.1478 RANDOM 26.409
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] 7.05 7.05 -14.1
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.543 r_dihedral_angle_2_deg 30.022 r_sphericity_bonded 24.356 r_rigid_bond_restr 19.77 r_dihedral_angle_4_deg 17.56 r_dihedral_angle_3_deg 13.498 r_dihedral_angle_1_deg 7.573 r_angle_refined_deg 1.645 r_angle_other_deg 1.384 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.543 r_dihedral_angle_2_deg 30.022 r_sphericity_bonded 24.356 r_rigid_bond_restr 19.77 r_dihedral_angle_4_deg 17.56 r_dihedral_angle_3_deg 13.498 r_dihedral_angle_1_deg 7.573 r_angle_refined_deg 1.645 r_angle_other_deg 1.384 r_chiral_restr 0.104 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.004 r_bond_other_d 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3241 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 95
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement DPS data reduction