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Crystal Structure of RPTP alpha
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 MES, PEG 20000, DTT
Crystal Properties Matthews coefficient Solvent content 2.88 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.72 α = 90 b = 112.11 β = 90 c = 136.37 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 PIXEL DECTRIS PILATUS3 6M 2017-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97741 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 30 100 0.086 0.094 0.037 0.998 10.6 6.2 148737
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 100 0.877 0.966 0.401 0.751 5.7
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 1YFO 1.8 30 141157 7392 99.88 0.1568 0.155 0.1657 0.191 0.1996 RANDOM 35.426
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] -1.07 1.59 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.111 r_dihedral_angle_4_deg 14.946 r_dihedral_angle_3_deg 12.69 r_dihedral_angle_1_deg 5.69 r_angle_refined_deg 1.476 r_angle_other_deg 1.327 r_chiral_restr 0.078 r_bond_refined_d 0.006 r_bond_other_d 0.002 r_gen_planes_refined 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.111 r_dihedral_angle_4_deg 14.946 r_dihedral_angle_3_deg 12.69 r_dihedral_angle_1_deg 5.69 r_angle_refined_deg 1.476 r_angle_other_deg 1.327 r_chiral_restr 0.078 r_bond_refined_d 0.006 r_bond_other_d 0.002 r_gen_planes_refined 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9420 Nucleic Acid Atoms Solvent Atoms 1529 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction MOSFLM data reduction