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P21B crystal structure of R1-R7 of Murine MVP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GF5 PDB ENTRY 3GF5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 277 20% PEG 5000, 0.1M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.76 55.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.776 α = 90 b = 60.087 β = 95.34 c = 68.628 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 315 2007-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.979 ESRF ID23-1
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 3 30 98.9 8990 8896 2 1
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 3 3.077 95.5
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 3GF5 3 29.7 8990 8896 454 96.57 0.25844 0.25705 0.255 0.28703 0.2799 RANDOM 45.395
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] -0.74 0.48 0.31 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.407 r_dihedral_angle_3_deg 13.49 r_dihedral_angle_4_deg 7.119 r_dihedral_angle_1_deg 3.341 r_angle_refined_deg 0.768 r_nbtor_refined 0.29 r_nbd_refined 0.138 r_symmetry_hbond_refined 0.109 r_scangle_it 0.104 r_symmetry_vdw_refined 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.407 r_dihedral_angle_3_deg 13.49 r_dihedral_angle_4_deg 7.119 r_dihedral_angle_1_deg 3.341 r_angle_refined_deg 0.768 r_nbtor_refined 0.29 r_nbd_refined 0.138 r_symmetry_hbond_refined 0.109 r_scangle_it 0.104 r_symmetry_vdw_refined 0.099 r_xyhbond_nbd_refined 0.073 r_scbond_it 0.059 r_chiral_restr 0.043 r_mcangle_it 0.041 r_mcbond_it 0.023 r_bond_refined_d 0.005 r_gen_planes_refined 0.001 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2959 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling