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Crystal Structure of Human Osteoclast Stimulating Factor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EHQ PDB ENTRY 3EHQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 12% PEG20000, 0.1M MES, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.69 27.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.306 α = 61.75 b = 57.935 β = 76.53 c = 60.477 γ = 90.08
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 MAR scanner 345 mm plate mirrors 2005-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.95 51.367 89.9 0.044 0.044 11.634 2 42702 21394
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.95 2.06 91.2 0.15 0.15 4.8 2 3159
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 3EHQ 1.95 20 21388 1102 89.99 0.181 0.178 0.1812 0.239 0.2371 RANDOM 18.185
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] 0.38 0.08 0.09 0.03 -0.1 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.748 r_dihedral_angle_4_deg 13.877 r_dihedral_angle_3_deg 13.753 r_dihedral_angle_1_deg 5.268 r_scangle_it 2.464 r_scbond_it 1.493 r_angle_refined_deg 1.037 r_mcangle_it 1.003 r_mcbond_it 0.538 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.748 r_dihedral_angle_4_deg 13.877 r_dihedral_angle_3_deg 13.753 r_dihedral_angle_1_deg 5.268 r_scangle_it 2.464 r_scbond_it 1.493 r_angle_refined_deg 1.037 r_mcangle_it 1.003 r_mcbond_it 0.538 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2761 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection