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Structure of a putative nucleotide phosphatase from Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Cr dataset at wavelength of 2.27 A, with a Rigaku MicroMax-007 HF generator and a Cr Raxis4++ detector. This was subsequently refined using a Cu-wavelength dataset deposited here.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 0.1M Bis-Tris pH6.5, 25 PEG 2K MME (monomethyl ether)
cryoprotected with 25% ethylene glycol
, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 1.99 38.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.474 α = 90 b = 64.664 β = 90 c = 67.708 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 IMAGE PLATE RIGAKU RAXIS HTC mirrors 2008-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.54178
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 1.6 23.38 95.5 0.077 0.077 14.95 5.7 34511 -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) 1.6 1.66 97.4 0.347 2.7 1.9
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 SAD THROUGHOUT Cr dataset at wavelength of 2.27 A, with a Rigaku MicroMax-007 HF generator and a Cr Raxis4++ detector. This was subsequently refined using a Cu-wavelength dataset deposited here. 1.7 23.38 25924 2889 99.78 0.19722 0.19395 0.1915 0.22611 0.2236 RANDOM 17.81
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.939 r_dihedral_angle_4_deg 18.791 r_dihedral_angle_3_deg 13.916 r_dihedral_angle_1_deg 5.781 r_scangle_it 3.952 r_scbond_it 2.408 r_mcangle_it 1.427 r_angle_refined_deg 1.405 r_mcbond_it 0.773 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.939 r_dihedral_angle_4_deg 18.791 r_dihedral_angle_3_deg 13.916 r_dihedral_angle_1_deg 5.781 r_scangle_it 3.952 r_scbond_it 2.408 r_mcangle_it 1.427 r_angle_refined_deg 1.405 r_mcbond_it 0.773 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.258 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.192 r_metal_ion_refined 0.168 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.099 r_bond_refined_d 0.012 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_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 2152 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 18
Software Software Software Name Purpose CrystalClear data collection SHELXCD phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling