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X-ray Crystal Structure of the Hypothetical Phosphotyrosine Phosphatase MDP-1 of the Haloacid Dehalogenase Superfamily
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other HIGH RESOLUTION MODEL OF MDP-1 WITHOUT MAGNESIUM BOUND
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 291 PEG 3350, sodium acetate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 8.00
Crystal Properties Matthews coefficient Solvent content 2 39.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.524 α = 90 b = 57.651 β = 91.97 c = 76.621 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE RIGAKU RAXIS IV OSMIC MIRRORS 2003-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 76.58 93.8 0.061 19.6 3.3 48167 17.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.85 1.92 88.3 0.0485 2.8 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 HIGH RESOLUTION MODEL OF MDP-1 WITHOUT MAGNESIUM BOUND 1.9 76.58 47331 43298 4380 91.5 0.19 0.19 0.1906 0.236 0.2356 RANDOM 28.1
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] 9.7 0.67 -3.78 -5.92
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.6 c_scangle_it 3.05 c_scbond_it 2.12 c_mcangle_it 1.99 c_mcbond_it 1.32 c_angle_deg 1.3 c_improper_angle_d 0.82 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.6 c_scangle_it 3.05 c_scbond_it 2.12 c_mcangle_it 1.99 c_mcbond_it 1.32 c_angle_deg 1.3 c_improper_angle_d 0.82 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5212 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms 14
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing CNS refinement