X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 26% PEG 4000, 0.2M magnesium acetate, 6% butyrolactone, 0.1M MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.84 α = 90
b = 93.84 β = 90
c = 99.87 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR ADSC QUANTUM 315 -- 2008-08-04
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.977 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
2.5 100 99.3 0.078 -- -- 5.2 18214 18047 2.0 1.0 36.7
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)
2.5 2.64 100.0 0.3 -- 5.7 -- --

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 2.5 29.36 -- 1.0 18214 16981 913 99.27 0.2253 0.22341 0.22176 0.25389 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 2.5 2.565 -- 71 1216 0.288 0.306 -- 99.92
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 48.178
Anisotropic B[1][1] -0.02
Anisotropic B[1][2] -0.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.03
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 0.641
r_scbond_it 0.398
r_mcangle_it 0.374
r_mcbond_it 0.214
r_symmetry_hbond_refined 0.119
r_bond_refined_d 0.006
r_angle_refined_deg 0.855
r_dihedral_angle_1_deg 4.281
r_dihedral_angle_2_deg 32.565
r_dihedral_angle_3_deg 14.73
r_dihedral_angle_4_deg 13.775
r_chiral_restr 0.056
r_gen_planes_refined 0.002
r_nbd_refined 0.173
r_nbtor_refined 0.292
r_xyhbond_nbd_refined 0.114
r_symmetry_vdw_refined 0.125
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3677
Nucleic Acid Atoms 251
Heterogen Atoms 0
Solvent Atoms 41

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
REFMAC 5.2.0019 Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
REFMAC version: 5.2.0019 model building
ADSC version: Quantum data collection