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Structure of Human Glioma Pathogenesis-related Protein 1 Reveals Unique loops and surface motifs.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q2R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 0.085M MES, 25.5% w/v PEG 5000 MME, 0.17M Ammonium sulfate 15% v/v glycerol, pH 6.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.82 56.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.077 α = 90 b = 79.532 β = 90 c = 38.849 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 100 CCD OXFORD ONYX CCD 2010-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.514
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 29.04 99.9 23229 3 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.95 99.4 3.2 4.9 16237
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 3Q2R 1.85 27.79 21977 1187 99.75 0.13662 0.13402 0.1423 0.18421 0.1871 RANDOM 20.46
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] -0.75 -3.5 4.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.57 r_dihedral_angle_4_deg 13.186 r_dihedral_angle_3_deg 12.463 r_scangle_it 7.612 r_dihedral_angle_1_deg 6.922 r_scbond_it 5.287 r_mcangle_it 3.294 r_rigid_bond_restr 2.824 r_mcbond_it 2.128 r_angle_refined_deg 1.888
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.57 r_dihedral_angle_4_deg 13.186 r_dihedral_angle_3_deg 12.463 r_scangle_it 7.612 r_dihedral_angle_1_deg 6.922 r_scbond_it 5.287 r_mcangle_it 3.294 r_rigid_bond_restr 2.824 r_mcbond_it 2.128 r_angle_refined_deg 1.888 r_chiral_restr 0.151 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1532 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 24
Software Software Software Name Purpose CrysalisPro data collection PHASER phasing REFMAC refinement CrysalisPro data reduction SCALA data scaling