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Crystal structure of RNA 3'-terminal phosphate cyclase, an ubiquitous enzyme with unusual topology
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QMI PDB ENTRY 1QMI, CHAIN A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 THE PROTEIN WAS CRYSTALLIZED FROM 13-15% MPEG 2000, 200 MM NA-CITRATE PH 4.0, 200 MM TRIS/HCL PH 8.0, 2 MM DTT. PROTEIN CONCENTRATION WAS CA. 15 MG/ML.
Crystal Properties Matthews coefficient Solvent content 2.84 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.8 α = 90 b = 133.5 β = 90 c = 51 γ = 90
Symmetry Space Group P 21 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 105 IMAGE PLATE MARRESEARCH 1998-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9B NSLS X9B
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 2.1 20 97.2 0.043 11.3 3.2 50057 -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) 1 2.1 2.17 83.4 0.268 3.6 2.8
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 1QMI, CHAIN A 2.1 10 48203 2286 93.6 0.207 0.204 0.1839 0.276 0.2423 RANDOM 37.1
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]
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 21.1 p_staggered_tor 17.5 p_scangle_it 4.6 p_planar_tor 4.3 p_mcangle_it 3.8 p_scbond_it 3 p_mcbond_it 2.6 p_multtor_nbd 0.261 p_singtor_nbd 0.196 p_chiral_restr 0.185
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 21.1 p_staggered_tor 17.5 p_scangle_it 4.6 p_planar_tor 4.3 p_mcangle_it 3.8 p_scbond_it 3 p_mcbond_it 2.6 p_multtor_nbd 0.261 p_singtor_nbd 0.196 p_chiral_restr 0.185 p_xyhbond_nbd 0.171 p_planar_d 0.056 p_angle_d 0.046 p_plane_restr 0.029 p_bond_d 0.022 p_angle_deg p_hb_or_metal_coord p_xhyhbond_nbd p_orthonormal_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4971 Nucleic Acid Atoms Solvent Atoms 424 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing