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The structure of UBR box (native2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NIT PDB ENTRY 3NIT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 0.02M calcium chloride dehydrate, 0.1M sodium acetate trihydrate pH 4.8, 30%(v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.17 43.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.576 α = 90 b = 44.576 β = 90 c = 140.055 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAC Science DIP-2030 2009-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6B 1.1000 PAL/PLS 6B
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 1.68 50 100 0.091 9.9 7.6 35555
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) 1.68 1.74 99.9 0.521 6.8 3495
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 3NIT 1.68 25.94 35466 1778 99.99 0.1944 0.1929 0.198 0.2214 0.2204 RANDOM 25.003
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] -0.05 -0.03 -0.05 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.573 r_dihedral_angle_4_deg 12.055 r_dihedral_angle_3_deg 11.965 r_dihedral_angle_1_deg 5.412 r_scangle_it 1.931 r_scbond_it 1.284 r_angle_refined_deg 1.025 r_mcangle_it 1.025 r_mcbond_it 0.599 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.573 r_dihedral_angle_4_deg 12.055 r_dihedral_angle_3_deg 11.965 r_dihedral_angle_1_deg 5.412 r_scangle_it 1.931 r_scbond_it 1.284 r_angle_refined_deg 1.025 r_mcangle_it 1.025 r_mcbond_it 0.599 r_nbtor_refined 0.293 r_symmetry_vdw_refined 0.208 r_nbd_refined 0.19 r_symmetry_hbond_refined 0.135 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.07 r_metal_ion_refined 0.019 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2542 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing