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S120G mutant of human nucleoside diphosphate kinase A complexed with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UCN PDB ENTRY 1UCN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 2.4 M AMMONIUM SULPHATE, 10 MM ADP, 20 MM MGCL2, 4 MM DTT, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.9 56.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.824 α = 90 b = 114.824 β = 90 c = 89.719 γ = 90
Symmetry Space Group P 41 21 2
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 MARRESEARCH 2004-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.980 ESRF BM30A
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 2.402 40 97.1 0.1 21.4 10.9 22088 22088 49.109
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 2.402 2.53 86.7 0.4 4 8.4
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 (All) 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 1UCN 2.402 40 22088 22088 1192 97.09 0.22078 0.22078 0.21784 0.2249 0.27725 0.2882 RANDOM 48.111
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] -0.06 -0.06 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.714 r_dihedral_angle_4_deg 20.984 r_dihedral_angle_3_deg 14.151 r_dihedral_angle_1_deg 5.948 r_angle_other_deg 2.315 r_scangle_it 1.878 r_scbond_it 1.48 r_angle_refined_deg 1.256 r_mcbond_it 1.027 r_mcangle_it 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.714 r_dihedral_angle_4_deg 20.984 r_dihedral_angle_3_deg 14.151 r_dihedral_angle_1_deg 5.948 r_angle_other_deg 2.315 r_scangle_it 1.878 r_scbond_it 1.48 r_angle_refined_deg 1.256 r_mcbond_it 1.027 r_mcangle_it 0.94 r_symmetry_vdw_refined 0.441 r_nbd_other 0.207 r_nbd_refined 0.197 r_symmetry_vdw_other 0.192 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.165 r_symmetry_hbond_refined 0.152 r_nbtor_other 0.087 r_chiral_restr 0.068 r_mcbond_other 0.025 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3588 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 81
Software Software Software Name Purpose MAR345 data collection REFMAC refinement MOSFLM data reduction CCP4 data scaling