X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 293.0
Details 50 mM Na Cacodylate, 40 mM Magnesium Acetate, 10% MPD, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.28 α = 90
b = 43.28 β = 90
c = 89.38 γ = 90
Symmetry
Space Group P 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-04-10
Diffraction Radiation
Monochromator Protocol
channel cut ESRF monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.974 ESRF ID14-4

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
2 30.6 99.8 0.072 -- -- 10.56 -- 6220 -- -- 43.8
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)
2.0 2.05 99.3 0.455 -- 2.88 3.7 813

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
SAD 2.0 30.6 -- -- -- 5923 288 99.84 0.22922 0.22922 0.22614 0.29351 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 2.0 2.05 813 16 430 0.29 0.293 -- 99.33
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 54.05
Anisotropic B[1][1] 0.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.22
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 44.606
r_mcbond_it 1.026
r_angle_refined_deg 2.064
r_scangle_it 4.588
r_dihedral_angle_3_deg 21.884
r_dihedral_angle_1_deg 6.941
r_chiral_restr 0.143
r_gen_planes_refined 0.015
r_bond_refined_d 0.027
r_dihedral_angle_4_deg 6.797
r_scbond_it 2.984
r_mcangle_it 1.742
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.188
Luzzati ESD (R-Free Set) 0.189
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 577
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 22

Software

Software
Software Name Purpose
DNA data collection
SHELXD phasing
REFMAC refinement version: 5.5.0110
XDS data reduction
XSCALE data scaling