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 Tris, PEG 3350, sodium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 105.64 α = 90
b = 105.64 β = 90
c = 235.56 γ = 90
Symmetry
Space Group P 43 21 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 SSRL BEAMLINE BL9-2 1.000 SSRL BL9-2

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
3.5 95 99.3 0.064 -- -- 6.7 -- 16292 -- -- 88.9
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)
3.5 3.69 99.3 0.381 -- 6.0 6.8 --

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 3.5 20.0 -- 0.0 -- 16292 876 98.41 0.29193 0.29193 0.29167 0.29683 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 3.5 3.588 -- 55 1183 0.383 0.37 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model TLS refinement used
Mean Isotropic B 44.801
Anisotropic B[1][1] 8.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 8.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -16.09
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.108
r_nbd_other 0.278
r_nbd_refined 0.295
r_gen_planes_other 0.004
r_gen_planes_refined 0.008
r_chiral_restr 0.13
r_dihedral_angle_3_deg 21.23
r_dihedral_angle_1_deg 5.003
r_angle_other_deg 1.332
r_angle_refined_deg 2.282
r_bond_other_d 0.003
r_bond_refined_d 0.023
r_xyhbond_nbd_refined 0.258
r_xyhbond_nbd_other 0.166
r_symmetry_vdw_refined 0.445
r_symmetry_vdw_other 0.42
r_symmetry_hbond_refined 0.659
r_mcbond_it 0.851
r_mcangle_it 1.636
r_scbond_it 1.879
r_scangle_it 3.383
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7887
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