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Crystal structure of ADP bound to MAP KAP kinase 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NZK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 296 2.0M Ammonium Sulfate, pH unbuffered, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 3.7 66.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 253.049 α = 90 b = 253.049 β = 90 c = 253.049 γ = 90
Symmetry Space Group F 41 3 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 ADSC QUANTUM 4 mirrors 2002-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 ALS 5.0.1
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 3 25 99.4 0.035 32.1 6.96 14402 14313
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 3 3.11 98.4 0.773 2.29 21 1385
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1NZK 3 20 2 13470 12796 674 93.91 0.26981 0.25913 0.25913 0.29237 RANDOM 86.442
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_scangle_it 28.648 r_scbond_it 22.053 r_mcangle_it 14.07 r_mcbond_it 10.649 r_dihedral_angle_1_deg 2.922 r_angle_refined_deg 1.649 r_symmetry_vdw_refined 0.388 r_symmetry_hbond_refined 0.352 r_nbd_refined 0.319 r_xyhbond_nbd_refined 0.189
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 28.648 r_scbond_it 22.053 r_mcangle_it 14.07 r_mcbond_it 10.649 r_dihedral_angle_1_deg 2.922 r_angle_refined_deg 1.649 r_symmetry_vdw_refined 0.388 r_symmetry_hbond_refined 0.352 r_nbd_refined 0.319 r_xyhbond_nbd_refined 0.189 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2180 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling AMoRE phasing