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Crystal structure of INPP5B in complex with biphenyl 3,3',4,4',5,5'- hexakisphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N9V PDB ENTRY 3N9V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.2 10% GLYCEROL, 25% PROPANEDIOL AND 0.1 M SODIUM/POTASSIUM PHOSPHATE PH 6.2
Crystal Properties Matthews coefficient Solvent content 4.96 75.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.975 α = 90 b = 96.975 β = 90 c = 152.142 γ = 90
Symmetry Space Group P 41 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 MARMOSAIC 225 mm CCD MIRRORS 2011-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 2.89 34.29 99.9 0.07 21.2 7 16922 -3
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 2.89 3.05 100 0.84 2.2 7.2
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 3N9V 2.89 34.29 16012 858 99.87 0.19826 0.197 0.1939 0.22324 0.2237 RANDOM 71.185
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] -1.25 -1.25 2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.76 r_dihedral_angle_4_deg 16.177 r_dihedral_angle_3_deg 14.137 r_dihedral_angle_1_deg 5.705 r_angle_refined_deg 1.191 r_scangle_it 1.132 r_angle_other_deg 0.771 r_scbond_it 0.641 r_mcangle_it 0.456 r_mcbond_it 0.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.76 r_dihedral_angle_4_deg 16.177 r_dihedral_angle_3_deg 14.137 r_dihedral_angle_1_deg 5.705 r_angle_refined_deg 1.191 r_scangle_it 1.132 r_angle_other_deg 0.771 r_scbond_it 0.641 r_mcangle_it 0.456 r_mcbond_it 0.237 r_chiral_restr 0.064 r_mcbond_other 0.03 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 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_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 2545 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing