X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.7
Temperature 293.0
Details 100 mM Na cacodylate, 400 mM KCl, 10 mM CaCl2, 15% (w/v) PEG4000, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 71.31 α = 90
b = 79.34 β = 101.99
c = 114.07 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirrors 2006-06-23
Diffraction Radiation
Monochromator Protocol
Diamond (111), Ge (220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-2 0.93300 ESRF ID14-2

Data Collection

Overall
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
3.2 64.7 99.2 -- 0.092 -- 3.9 20744 20578 0.0 0.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
3.2 3.37 99.2 -- 0.388 3.3 3.9 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 3.2 64.68 0.0 0.0 20794 20563 1054 98.89 0.242 0.242 0.24 0.285 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 3.2 3.283 -- 76 1432 0.288 0.349 -- 98.76
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 86.721
Anisotropic B[1][1] -7.56
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -4.77
Anisotropic B[2][2] 3.6
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.98
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 35.472
r_scbond_it 1.116
r_dihedral_angle_3_deg 21.476
r_gen_planes_refined 0.019
r_bond_refined_d 0.015
r_mcangle_it 0.961
r_angle_refined_deg 1.619
r_dihedral_angle_1_deg 5.317
r_mcbond_it 0.506
r_chiral_restr 0.073
r_scangle_it 1.95
r_dihedral_angle_4_deg 17.625
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1537
Nucleic Acid Atoms 4106
Heterogen Atoms 10
Solvent Atoms 0

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0066
PDB_EXTRACT data extraction version: 3.005
MxCuBE data collection
MOSFLM data reduction
SCALA data scaling
PHASER phasing