X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 298.0
Details 10% saturated Ammonium sulfate, 1mM DTT, 20mM Potassium phosphate , pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.99 α = 90
b = 77.99 β = 90
c = 224.72 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2008-10-27
Diffraction Radiation
Monochromator Protocol
Silicon (111) channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.983 ESRF ID23-1

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
2.25 74.95 99.9 0.079 0.079 -- 19.9 -- 20159 1.0 2.0 33.669
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)
2.25 2.37 100.0 0.286 0.286 10.8 20.9 2868

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 2.25 67.54 2.0 -- 20103 19048 1024 99.85 -- 0.21457 0.21164 0.27083 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 2.25 2.309 1353 89 1353 0.264 0.394 -- 99.93
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.159
Anisotropic B[1][1] 0.03
Anisotropic B[1][2] 0.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.04
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 1.123
r_angle_refined_deg 2.027
r_scangle_it 4.36
r_scbond_it 2.858
r_chiral_restr 0.136
r_gen_planes_refined 0.009
r_mcangle_it 2.076
r_dihedral_angle_1_deg 6.677
r_bond_refined_d 0.019
r_dihedral_angle_2_deg 35.501
r_dihedral_angle_3_deg 18.809
r_dihedral_angle_4_deg 22.565
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.285
Luzzati ESD (R-Free Set) 0.236
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2561
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 159

Software

Software
Software Name Purpose
MOLREP phasing
REFMAC refinement version: 5.5.0072
MOSFLM data reduction
SCALA data scaling