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Structure of human cystatin D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CEW PDB ENTRY 1CEW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 Tris-HCl, PEG400, (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.75 54.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.9 α = 90 b = 84.37 β = 90 c = 47.65 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 291 IMAGE PLATE MARRESEARCH 1999-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.5 30 94.5 0.076 4.2 5243 4955 45.1
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) 2.5 2.59 96.8 0.252 467
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 1CEW 2.5 28.16 5220 4835 501 92.6 0.191 0.191 0.1883 0.229 0.2297 RANDOM 44.6
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] -5.65 -2.89 8.54
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.7 c_scangle_it 15.69 c_scbond_it 11.38 c_mcangle_it 7.7 c_mcbond_it 4.86 c_angle_deg 1.3 c_improper_angle_d 0.87 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.7 c_scangle_it 15.69 c_scbond_it 11.38 c_mcangle_it 7.7 c_mcbond_it 4.86 c_angle_deg 1.3 c_improper_angle_d 0.87 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_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 912 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms
Software Software Software Name Purpose CNS refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing