3S7A

Human dihydrofolate reductase binary complex with PT684


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U72PDB ENTRY 1U72

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.928730% ammonium sulfate, 100 mM K2PO4, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties
Matthews coefficientSolvent content
2.2846.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.588α = 90
b = 55.106β = 90
c = 64.827γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDMARMOSAIC 325 mm CCDmirrors2011-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.975SSRLBL9-2

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.84295.40.230.0947.76.718704187042233.2
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)RedundancyNumber Unique Reflections (All)
11.81.974.70.310.1572.64.61964

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1U721.8422178291688490595.110.239160.236860.2835RANDOM24.003
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.357
r_dihedral_angle_3_deg19.273
r_dihedral_angle_4_deg14.324
r_dihedral_angle_1_deg7.427
r_scangle_it5.134
r_scbond_it3.601
r_mcangle_it2.24
r_angle_refined_deg2.055
r_mcbond_it1.289
r_chiral_restr0.162
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.357
r_dihedral_angle_3_deg19.273
r_dihedral_angle_4_deg14.324
r_dihedral_angle_1_deg7.427
r_scangle_it5.134
r_scbond_it3.601
r_mcangle_it2.24
r_angle_refined_deg2.055
r_mcbond_it1.289
r_chiral_restr0.162
r_bond_refined_d0.022
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1502
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms60

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling