X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 3 M NaOAc pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 116.03 α = 90
b = 121.43 β = 90
c = 123.3 γ = 90
Symmetry
Space Group I 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2012-06-25
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1

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
1.86 86.5 98.1 0.065 0.065 -- 6.6 -- 71548 3.2 3.2 --
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)
1.86 1.96 87.6 0.065 -- 3.2 6.5 --

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 1.86 58.0 -- -- 71549 67939 3609 98.08 -- 0.16624 0.1651 0.18772 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 1.862 1.91 -- 192 4001 0.254 0.255 -- 81.75
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 24.897
Anisotropic B[1][1] 2.14
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.14
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.016
r_chiral_restr 0.128
r_dihedral_angle_4_deg 19.905
r_dihedral_angle_3_deg 12.262
r_gen_planes_refined 0.009
r_dihedral_angle_1_deg 6.03
r_angle_refined_deg 1.619
r_dihedral_angle_2_deg 29.321
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.101
Luzzati ESD (R-Free Set) 0.099
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3998
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 480

Software

Software
Software Name Purpose
DNA data collection
SHELXS phasing
REFMAC refinement version: 5.6.0117
XDS data reduction
SCALA data scaling