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Crystal structure of GMP synthetase PH1347 from Pyrococcus horikoshii OT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 278 30%(v/v) PEG400, 100mM Tris-HCl(pH 8.4), 200mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.32 46.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.903 α = 90 b = 82.212 β = 90 c = 111.565 γ = 90
Symmetry Space Group P 21 21 21
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 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 1.79 50 0.052 8.8 60634
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 1.79 1.85 0.076 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.79 50 57488 3071 98.22 0.21182 0.21002 0.209 0.24612 0.2476 RANDOM 21.387
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] 0.44 0.49 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.902 r_dihedral_angle_4_deg 20.078 r_dihedral_angle_3_deg 13.657 r_dihedral_angle_1_deg 5.133 r_scangle_it 4.149 r_scbond_it 2.562 r_mcangle_it 1.463 r_angle_refined_deg 1.361 r_mcbond_it 0.991 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.902 r_dihedral_angle_4_deg 20.078 r_dihedral_angle_3_deg 13.657 r_dihedral_angle_1_deg 5.133 r_scangle_it 4.149 r_scbond_it 2.562 r_mcangle_it 1.463 r_angle_refined_deg 1.361 r_mcbond_it 0.991 r_nbtor_refined 0.309 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.195 r_xyhbond_nbd_refined 0.121 r_symmetry_hbond_refined 0.115 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 4528 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing