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Crystal Structure of a Collagen VIII NC1 Domain Trimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GR3 PDB ENTRY 1GR3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 1.7 M AMMONIUM SULFATE, 4 % (V/V)ISOPROPANOL, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.1 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.59 α = 90 b = 82.55 β = 90 c = 89.94 γ = 90
Symmetry Space Group P 21 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 IMAGE PLATE MARRESEARCH OSMIC MIRRORS 2002-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 1.9 20 98.9 0.087 15.7 5.6 37444 14.1
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 1.9 1.99 98.9 0.24 6.7 5.3
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 PDB ENTRY 1GR3 1.9 20 37444 3756 98.7 0.185 0.185 0.1835 0.209 0.208 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.6 c_mcangle_it 1.8 c_scbond_it 1.8 c_angle_deg 1.5 c_mcbond_it 1.2 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.6 c_mcangle_it 1.8 c_scbond_it 1.8 c_angle_deg 1.5 c_mcbond_it 1.2 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3120 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 37
Software Software Software Name Purpose CNS refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing