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Crystal Structure of Human CDK7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HCK Human CDK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 277 Na Citrate, Na Acetate, PEG 4000, glycerol, NDSB201, ATP, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K
Crystal Properties Matthews coefficient Solvent content 3.63 65.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.501 α = 90 b = 191.635 β = 94.4 c = 75.794 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 CCD ADSC QUANTUM 4 2003-11-22 M SINGLE WAVELENGTH 2 1 100 CCD MARRESEARCH Microfocus beamline ID13 at ESRF 2003-12-06
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9756 ESRF ID29 2 SYNCHROTRON ESRF BEAMLINE ID13 0.9789 ESRF ID13
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 2.96 49.45 92.9 0.129 0.129 9.5 3.8 38122 35416 1 73.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.02 3.18 70.1 0.466 0.466 1.6 1.7 3851
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 Human CDK2 3.02 49.45 33271 33271 1757 95.48 0.21659 0.21659 0.21274 0.21 0.2879 0.2849 RANDOM 44.013
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] 4.22 -0.05 -2.56 -1.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.62 r_dihedral_angle_3_deg 24.144 r_dihedral_angle_4_deg 19.748 r_dihedral_angle_1_deg 8.773 r_scangle_it 2.453 r_angle_refined_deg 1.923 r_scbond_it 1.463 r_mcangle_it 1.277 r_mcbond_it 0.698 r_symmetry_hbond_refined 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.62 r_dihedral_angle_3_deg 24.144 r_dihedral_angle_4_deg 19.748 r_dihedral_angle_1_deg 8.773 r_scangle_it 2.453 r_angle_refined_deg 1.923 r_scbond_it 1.463 r_mcangle_it 1.277 r_mcbond_it 0.698 r_symmetry_hbond_refined 0.35 r_nbtor_refined 0.335 r_symmetry_vdw_refined 0.312 r_nbd_refined 0.284 r_xyhbond_nbd_refined 0.225 r_chiral_restr 0.136 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9164 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 124
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling