X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 295.0
Details 0.1 M TEA, 1.3 M sodium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 116.65 α = 90
b = 116.65 β = 90
c = 216.78 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2000-11-18
Diffraction Radiation
Monochromator Protocol
bendable mirror and asymmetrically cut Si(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I711 0.946 MAX II I711

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
3.3 20 -- 0.131 -- -- 5.3 23549 22527 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)
3.3 3.42 96.6 -- -- -- -- --

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 3.29 20.0 -- -- 21372 21512 1162 96.9 -- 0.208 0.20508 0.26209 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 3.286 3.369 -- 81 1405 0.206 0.317 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 19.628
Anisotropic B[1][1] -0.21
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.41
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.082
r_symmetry_vdw_refined 0.188
r_symmetry_hbond_refined 0.129
r_scbond_it 1.186
r_bond_refined_d 0.01
r_angle_refined_deg 1.201
r_gen_planes_refined 0.003
r_mcbond_it 0.45
r_dihedral_angle_1_deg 5.398
r_scangle_it 2.097
r_xyhbond_nbd_refined 0.141
r_mcangle_it 0.887
r_nbd_refined 0.222
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6399
Nucleic Acid Atoms 0
Heterogen Atoms 186
Solvent Atoms 2

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (TRUNCATE) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC refinement
DENZO data collection
AMoRE model building
TRUNCATE data reduction