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Crystal Structure of Golgi Phosphoprotein 3 N-term Truncation Variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZIH PDB entry 2ZIH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 0.9 M (NH4)2SO4, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.84 67.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.369 α = 90 b = 174.369 β = 90 c = 174.369 γ = 90
Symmetry Space Group I 4 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2008-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97951 APS 23-ID-B
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 2.9 50 98.3 0.133 7.8 3.6 10180 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) 2.9 3 99.6 0.586 2.4 3.6 994
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 2ZIH 2.9 50 10149 491 97.99 0.215 0.213 0.2067 0.266 0.2555 RANDOM 38.227
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 r_dihedral_angle_2_deg 36.79 r_dihedral_angle_4_deg 21.88 r_dihedral_angle_3_deg 19.743 r_dihedral_angle_1_deg 13.193 r_scangle_it 4.517 r_scbond_it 2.807 r_angle_refined_deg 1.779 r_mcangle_it 1.721 r_mcbond_it 0.854 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.79 r_dihedral_angle_4_deg 21.88 r_dihedral_angle_3_deg 19.743 r_dihedral_angle_1_deg 13.193 r_scangle_it 4.517 r_scbond_it 2.807 r_angle_refined_deg 1.779 r_mcangle_it 1.721 r_mcbond_it 0.854 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1900 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction