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_gen_planes_refined 0.009
r_chiral_restr 0.128
r_dihedral_angle_4_deg 19.905
r_dihedral_angle_3_deg 12.262
r_dihedral_angle_2_deg 29.321
r_dihedral_angle_1_deg 6.03
r_angle_refined_deg 1.619
r_bond_refined_d 0.016
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

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
SHELXS Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
SHELXS model building
DNA data collection