3NP0

Crystal Structure of Pd(allyl)/apo-E45C/H49A/R52H-rHLFr


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DAT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293ammonium sulfate, cadmium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1260.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 180.959α = 90
b = 180.959β = 90
c = 180.959γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.0000SPring-8BL38B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.483098.30.0649.841911
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.481.5388.70.2864.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1DAT1.4819.2939184207096.820.198950.198410.20954RANDOM16.578
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.985
r_dihedral_angle_4_deg17.91
r_dihedral_angle_3_deg14.19
r_dihedral_angle_1_deg4.479
r_scangle_it3.069
r_scbond_it1.82
r_angle_refined_deg1.613
r_mcangle_it1.172
r_mcbond_it0.65
r_chiral_restr0.357
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.985
r_dihedral_angle_4_deg17.91
r_dihedral_angle_3_deg14.19
r_dihedral_angle_1_deg4.479
r_scangle_it3.069
r_scbond_it1.82
r_angle_refined_deg1.613
r_mcangle_it1.172
r_mcbond_it0.65
r_chiral_restr0.357
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1364
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms67

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
SCALEPACKdata scaling