X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 291.0
Details 1.35 M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50 mM Mes-NaOH, 1mM EDTA, pH 6.5, vapor diffusion, hanging drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 160.09 α = 90
b = 160.09 β = 90
c = 123.94 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
AREA DETECTOR ADSC -- 2010-04-26
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I02 0.97950 Diamond I02

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
2.55 39.21 98.9 -- 0.084 -- 5.5 -- 52142 -3.0 -3.0 --
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)
2.55 2.69 99.0 0.931 0.931 2.0 5.4 7536

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 2.55 39.21 -- 0.0 -- 52062 2627 98.33 0.2 0.1986 0.1973 0.2217 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 2.55 2.616 -- 194 3591 0.353 0.387 -- 98.57
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 58.3457
Anisotropic B[1][1] 1.46
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.46
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.92
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.496
r_dihedral_angle_1_deg 6.015
r_mcbond_it 0.725
r_dihedral_angle_2_deg 34.983
r_chiral_restr 0.084
r_dihedral_angle_4_deg 18.176
r_scangle_it 2.99
r_mcangle_it 1.391
r_scbond_it 1.777
r_gen_planes_refined 0.006
r_dihedral_angle_3_deg 15.897
r_bond_refined_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4339
Nucleic Acid Atoms 732
Heterogen Atoms 39
Solvent Atoms 274

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling version: 3.3.16
REFMAC refinement version: 5.5.0109
PDB_EXTRACT data extraction version: 3.10
ADSC data collection version: Quantum
PHASER phasing