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Crystal structure of unliganded SRA domain of mouse Np95
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BI7 PDB ENTRY 3BI7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 0.1M Tris-HCl (pH8.0), 0.1M Sodium acetate, 12% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.88 57.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.334 α = 91.11 b = 67.013 β = 65.01 c = 69.572 γ = 84.48
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 2008-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 1.77 50 95.4 0.071 3.8 96644 23.02
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) 1 1.77 1.83 77.3 0.372 2.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3BI7 1.77 29.31 91798 4845 95.24 0.18797 0.18648 0.21678 0.2363 RANDOM 25.491
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] -0.6 0.45 0.83 -0.27 0.46 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.55 r_dihedral_angle_4_deg 18.123 r_dihedral_angle_3_deg 12.704 r_dihedral_angle_1_deg 5.971 r_scangle_it 3.293 r_scbond_it 2.296 r_angle_refined_deg 1.401 r_mcangle_it 1.389 r_mcbond_it 1.233 r_angle_other_deg 0.995
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.55 r_dihedral_angle_4_deg 18.123 r_dihedral_angle_3_deg 12.704 r_dihedral_angle_1_deg 5.971 r_scangle_it 3.293 r_scbond_it 2.296 r_angle_refined_deg 1.401 r_mcangle_it 1.389 r_mcbond_it 1.233 r_angle_other_deg 0.995 r_symmetry_vdw_other 0.276 r_symmetry_vdw_refined 0.231 r_mcbond_other 0.227 r_nbd_other 0.216 r_nbd_refined 0.196 r_nbtor_refined 0.183 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.105 r_nbtor_other 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5917 Nucleic Acid Atoms Solvent Atoms 514 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing