X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RKD1RKD: RESIDUES 4-9, 44-93, 123-241 AND 254-309.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.8CRYSTALS WERE GROWN IN 22-33% PEG 2000, MONO-METHYLETHER AS PRECIPITANT AND BUFFERED TO PH 4.8 WITH 0.1 M NA ACETATE. CRYO-PROTECTANT: MOTHER LIQUID ALSO CONTAINING 15% ETHYLENEGLYCOL. SOAK-TIME: 2-3 MINUTES.
Crystal Properties
Matthews coefficientSolvent content
2.140.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.97α = 90
b = 61.97β = 90
c = 127.834γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS1998-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I711MAX III711

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
12.31596.40.05620.65.51264432
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)
12.32.3487.50.2356.75.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1RKD: RESIDUES 4-9, 44-93, 123-241 AND 254-309.2.315126441264461996.30.210.253RANDOM27
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]
-2.84-1.66-2.845.685
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d23.1
x_scangle_it2.5
x_scbond_it1.8
x_mcangle_it1.7
x_angle_deg1.5
x_mcbond_it1.1
x_improper_angle_d0.76
x_bond_d0.007
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d23.1
x_scangle_it2.5
x_scbond_it1.8
x_mcangle_it1.7
x_angle_deg1.5
x_mcbond_it1.1
x_improper_angle_d0.76
x_bond_d0.007
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2236
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms

Software

Software
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling