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T.thermophilus ribosomal protein L11 methyltransferase (PrmA) in space group P 21 21 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NXC pdb entry 1NXC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 1.7 M Ammonium sulfate, 85 mM HEPES-Na, pH 7.5, 1.7% w/v PEG400, 15% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.86 57.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.195 α = 90 b = 153.622 β = 90 c = 33.255 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 100 CCD ADSC QUANTUM 4 2006-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A NSLS X4A
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 2.3 50 96.8 0.082 15.4 3.7 29480 28554 -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 2.3 2.38 85.8 0.417 2.2 2.9 2530
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 1NXC 2.3 30 27095 1446 96.9 0.21139 0.20783 0.2042 0.27624 0.2672 RANDOM 48.57
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] 4.55 -2.1 -2.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.778 r_dihedral_angle_3_deg 20.344 r_dihedral_angle_4_deg 16.212 r_dihedral_angle_1_deg 7.031 r_scangle_it 3.121 r_scbond_it 1.963 r_angle_refined_deg 1.731 r_mcangle_it 1.45 r_mcbond_it 0.836 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.778 r_dihedral_angle_3_deg 20.344 r_dihedral_angle_4_deg 16.212 r_dihedral_angle_1_deg 7.031 r_scangle_it 3.121 r_scbond_it 1.963 r_angle_refined_deg 1.731 r_mcangle_it 1.45 r_mcbond_it 0.836 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.237 r_symmetry_vdw_refined 0.217 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.199 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3799 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling COMO phasing PHASER phasing