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Crystal structure of baculovirus RNA 5'-phosphatase complexed with phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I9T PDB entry 1I9T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 295 sodium/potassium phosphate, sodium acetate, guanidine hydrochloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.8 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.91 α = 90 b = 74.13 β = 92.38 c = 105.2 γ = 90
Symmetry Space Group P 1 21 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 CCD MARRESEARCH 2003-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 0.9479 APS 5ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.5 150 97.1 0.073 0.066 6.8 4.4 424098 97263 14.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.54 90.4 0.302 0.25 2.7 2.8 6308
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 (All) 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 1I9T 1.5 105.41 92370 4870 96.84 0.167 0.16702 0.1656 0.1661 0.19427 0.1944 RANDOM 14.41
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] -0.69 -0.38 -0.23 0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.878 r_dihedral_angle_4_deg 13.302 r_dihedral_angle_3_deg 11.962 r_dihedral_angle_1_deg 5.567 r_scangle_it 2.945 r_scbond_it 2.044 r_angle_refined_deg 1.233 r_mcangle_it 1.202 r_mcbond_it 1.082 r_angle_other_deg 0.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.878 r_dihedral_angle_4_deg 13.302 r_dihedral_angle_3_deg 11.962 r_dihedral_angle_1_deg 5.567 r_scangle_it 2.945 r_scbond_it 2.044 r_angle_refined_deg 1.233 r_mcangle_it 1.202 r_mcbond_it 1.082 r_angle_other_deg 0.779 r_symmetry_vdw_other 0.295 r_nbd_refined 0.22 r_nbtor_refined 0.183 r_nbd_other 0.182 r_mcbond_other 0.18 r_symmetry_vdw_refined 0.148 r_xyhbond_nbd_refined 0.136 r_symmetry_hbond_refined 0.136 r_nbtor_other 0.082 r_chiral_restr 0.069 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4120 Nucleic Acid Atoms Solvent Atoms 597 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction CCP4 data scaling AMoRE phasing