X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 298.0
Details 25% PEG 3350, 0.1M Tris-Cl pH 8.5 and 0.2M lithium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 87.86 α = 90
b = 57.73 β = 97.51
c = 118.11 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD mirrors 2010-10-23
Diffraction Radiation
Monochromator Protocol
Double crystal cryo-cooled Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 0.96801 APS 23-ID-B

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
2.99 50 99.6 0.095 -- -- 3.6 11921 11714 0.0 0.0 62.7
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)
2.995 3.05 98.0 0.388 -- 4.3 3.4 590

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 2.995 43.42 -- 0.0 11921 11349 568 99.03 0.3251 0.3251 0.32334 0.3593 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 2.995 3.073 776 33 776 0.39 0.343 -- 91.72
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 82.987
Anisotropic B[1][1] -1.3
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.72
Anisotropic B[2][2] 2.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.2
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 0.181
r_scbond_it 0.108
r_mcangle_it 0.106
r_mcbond_it 0.059
r_nbd_refined 0.166
r_gen_planes_refined 0.002
r_chiral_restr 0.062
r_dihedral_angle_4_deg 10.535
r_dihedral_angle_3_deg 14.516
r_dihedral_angle_2_deg 33.398
r_dihedral_angle_1_deg 3.944
r_angle_refined_deg 0.91
r_bond_refined_d 0.006
r_nbtor_refined 0.288
r_xyhbond_nbd_refined 0.088
r_symmetry_vdw_refined 0.212
r_symmetry_hbond_refined 0.028
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3280
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
PHASER model building
HKL-2000 data collection