X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 289.0
Details PEG 3350, sodium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.89 α = 90
b = 79.89 β = 90
c = 251.19 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
AREA DETECTOR -- -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 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
2.8 79 99.9 0.066 -- -- 6.8 19819 n/a -- -- 84.2
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)
2.8 2.95 -- 0.39 -- 4.6 7.1 --

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 2.8 20.0 -- 0.0 19819 19819 1075 99.96 0.25431 0.25431 0.25357 0.26783 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 2.8 2.871 -- 68 1416 0.322 0.381 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model TLS refinement used
Mean Isotropic B 50.316
Anisotropic B[1][1] 0.48
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.48
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.96
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_other 0.272
r_nbd_refined 0.282
r_gen_planes_other 0.006
r_gen_planes_refined 0.009
r_chiral_restr 0.113
r_dihedral_angle_3_deg 19.51
r_dihedral_angle_1_deg 4.618
r_angle_other_deg 0.932
r_angle_refined_deg 2.096
r_bond_other_d 0.001
r_bond_refined_d 0.023
r_xyhbond_nbd_refined 0.195
r_xyhbond_nbd_other 0.047
r_symmetry_vdw_refined 0.516
r_symmetry_vdw_other 0.294
r_symmetry_hbond_refined 0.558
r_mcbond_it 1.239
r_mcangle_it 2.307
r_scbond_it 2.641
r_scangle_it 4.532
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3837
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
AMoRE model building
SCALA data reduction
MOSFLM data collection