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Structure of the human collagen X NC1 trimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C28
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 1.6 M MGSO4, 0.1 M MES PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.24 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.36 α = 90 b = 78.36 β = 90 c = 141.036 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 293 IMAGE PLATE MARRESEARCH OSMIC MIRRORS 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 2 20 99.9 0.076 13.5 4.7 11537 26.2
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 2.1 100 0.385 4.1 4.7
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 1C28 2 20 11533 1193 99.9 0.186 0.186 0.1907 0.199 0.2026 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 2.8 c_mcangle_it 2.1 c_scbond_it 1.9 c_angle_deg 1.4 c_mcbond_it 1.3 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.8 c_mcangle_it 2.1 c_scbond_it 1.9 c_angle_deg 1.4 c_mcbond_it 1.3 c_bond_d 0.007 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 1057 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 29
Software Software Software Name Purpose CNS refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing