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Crystal structure of Nicotinic acid mononucleotide adenylyltransferase from Staphylococcus aureus: product bound form 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H29 PDB ENTRY 2H29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 10mg/ml protein, 50mM Hepes pH 7.2, 300mM KCl, 0.5mM TCEP, 1mM EDTA mixed in equal volume of 20% PEG8000(w/v), 100mM MES pH 6.0, 0.2M Ca(OAc)2
Crystal Properties Matthews coefficient Solvent content 2.91 57.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.303 α = 90 b = 83.649 β = 90 c = 99.113 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 175 IMAGE PLATE RIGAKU RAXIS IV 2005-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 30 99.4 0.099 25.3 6.1 35401 1
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 2.07 94.6 0.532 2.83 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 2H29 2.1 30 1 22357 29357 1544 99.9 0.202 0.2 0.1999 0.239 0.2386 RANDOM 28.76
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] -1.06 0.17 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.41 r_dihedral_angle_4_deg 21.942 r_dihedral_angle_3_deg 16.013 r_dihedral_angle_1_deg 6.005 r_scangle_it 4.023 r_scbond_it 2.759 r_mcangle_it 2.039 r_angle_refined_deg 1.746 r_mcbond_it 1.301 r_symmetry_hbond_refined 0.413
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.41 r_dihedral_angle_4_deg 21.942 r_dihedral_angle_3_deg 16.013 r_dihedral_angle_1_deg 6.005 r_scangle_it 4.023 r_scbond_it 2.759 r_mcangle_it 2.039 r_angle_refined_deg 1.746 r_mcbond_it 1.301 r_symmetry_hbond_refined 0.413 r_nbtor_refined 0.296 r_nbd_refined 0.19 r_xyhbond_nbd_refined 0.178 r_symmetry_vdw_refined 0.152 r_chiral_restr 0.143 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 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 3116 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling