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Crystal Structure of HePTP with an Open WPD Loop and Partially Depleted Active Site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O4S PDB entry 3O4S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277 1.7-1.9M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.26 45.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.015 α = 90 b = 38.995 β = 124.18 c = 83.713 γ = 90
Symmetry Space Group C 1 2 1
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 RIGAKU RAXIS IV++ RIGAKU OSMIC CONFOCAL OPTIC 2009-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5400
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.6 20 90.3 0.088 11.4 2.3 9939 8972 37.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.6 2.64 86.9 0.296 3.7 2 385
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB entry 3O4S 2.6 20 8530 8530 440 90.03 0.20159 0.19885 0.2527 0.2117 RANDOM 23.955
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] 1.38 0.46 -0.39 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.775 r_dihedral_angle_4_deg 17.848 r_dihedral_angle_3_deg 14.362 r_scangle_it 6.722 r_dihedral_angle_1_deg 4.971 r_scbond_it 4.757 r_mcangle_it 2.925 r_mcbond_it 1.769 r_angle_refined_deg 1.096 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.775 r_dihedral_angle_4_deg 17.848 r_dihedral_angle_3_deg 14.362 r_scangle_it 6.722 r_dihedral_angle_1_deg 4.971 r_scbond_it 4.757 r_mcangle_it 2.925 r_mcbond_it 1.769 r_angle_refined_deg 1.096 r_nbtor_refined 0.293 r_symmetry_hbond_refined 0.272 r_xyhbond_nbd_refined 0.178 r_nbd_refined 0.172 r_symmetry_vdw_refined 0.169 r_chiral_restr 0.062 r_bond_refined_d 0.01 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2225 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 27
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing