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Crystal structure of a putative gmp synthase subunit a protein (ta0944m) from thermoplasma acidophilum at 2.45 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QDL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 293 22.00% PEG 3350, 0.20M NP_Sodium Thiocyanate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 37.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 275.661 α = 90 b = 39.045 β = 90 c = 68.267 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 315 2005-02-25 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.00, 0.97971, 0.97947 ALS 8.2.2
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 2.24 66.27 78.6 0.053 0.053 9 3.2 29096
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 2.24 2.3 30.7 0.163 0.163 4.8 1.5
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD, Molecular replacement THROUGHOUT 1qdl 2.24 66.27 27616 1439 79.08 0.179 0.176 0.2078 0.246 0.2767 RANDOM 25.529
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] 1.29 -0.83 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.44 r_dihedral_angle_4_deg 17.237 r_dihedral_angle_3_deg 15.829 r_dihedral_angle_1_deg 5.487 r_scangle_it 3.293 r_scbond_it 2.092 r_angle_refined_deg 1.57 r_mcangle_it 1.047 r_angle_other_deg 0.983 r_mcbond_it 0.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.44 r_dihedral_angle_4_deg 17.237 r_dihedral_angle_3_deg 15.829 r_dihedral_angle_1_deg 5.487 r_scangle_it 3.293 r_scbond_it 2.092 r_angle_refined_deg 1.57 r_mcangle_it 1.047 r_angle_other_deg 0.983 r_mcbond_it 0.494 r_symmetry_vdw_refined 0.378 r_symmetry_vdw_other 0.227 r_nbd_refined 0.202 r_nbd_other 0.195 r_symmetry_hbond_refined 0.195 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.169 r_mcbond_other 0.153 r_nbtor_other 0.088 r_chiral_restr 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6283 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling MOLREP phasing SHARP phasing ARP/wARP model building SHELXD phasing