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Human 3'(2'), 5'-bisphosphate nucleotidase 1 (BPNT1) in complex with AMP, PO4 and Magnesium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JP4 PDB ENTRY 1JP4
Crystallization Crystal Properties Matthews coefficient Solvent content 1.81 31.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.98 α = 90 b = 67.664 β = 90 c = 100.394 γ = 90
Symmetry Space Group P 2 21 21
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 CCD 2009-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.8 19.52 99.5 0.09 20.3 13.5 30231
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 1.69 1.78 97.2 0.55 3.8 8.5
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 1JP4 1.8 19.52 24052 1284 99.9 0.146 0.144 0.1564 0.189 0.2011 RANDOM 12.01
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] 0.06 -0.04 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.615 r_dihedral_angle_4_deg 15.634 r_dihedral_angle_3_deg 13.503 r_dihedral_angle_1_deg 6.339 r_scangle_it 5.685 r_scbond_it 3.429 r_mcangle_it 2.176 r_angle_refined_deg 1.906 r_mcbond_it 1.239 r_angle_other_deg 1.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.615 r_dihedral_angle_4_deg 15.634 r_dihedral_angle_3_deg 13.503 r_dihedral_angle_1_deg 6.339 r_scangle_it 5.685 r_scbond_it 3.429 r_mcangle_it 2.176 r_angle_refined_deg 1.906 r_mcbond_it 1.239 r_angle_other_deg 1.065 r_chiral_restr 0.126 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2311 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing