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Crystal Structure Analysis of an NDP kinase from Pyrobaculum aerophilum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.65 53.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.022 α = 90 b = 72.041 β = 133.3 c = 104.993 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 4 mirrors 2000-10-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 0.9792, 0.9791, 0.9500 NSLS X8C
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 2.4 25 87.3 0.105 25584 22330
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.55 98.8
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 MAD THROUGHOUT 2.5 25 20785 1620 94.76 0.19201 0.18668 0.2052 0.25964 0.2713 RANDOM 37.065
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] -0.64 -0.82 0.62 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.963 r_dihedral_angle_4_deg 24.981 r_dihedral_angle_3_deg 20.308 r_dihedral_angle_1_deg 6.445 r_scangle_it 4.15 r_scbond_it 2.549 r_angle_refined_deg 1.886 r_mcangle_it 1.596 r_mcbond_it 0.948 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.963 r_dihedral_angle_4_deg 24.981 r_dihedral_angle_3_deg 20.308 r_dihedral_angle_1_deg 6.445 r_scangle_it 4.15 r_scbond_it 2.549 r_angle_refined_deg 1.886 r_mcangle_it 1.596 r_mcbond_it 0.948 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.242 r_symmetry_hbond_refined 0.214 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.115 r_bond_refined_d 0.019 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4242 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling SOLVE phasing