X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4
Temperature 291.0
Details 1.6 mM ammonium sulfate, 0.1 M citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.64 α = 90
b = 43.64 β = 90
c = 158.56 γ = 120
Symmetry
Space Group P 3 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2008-03-17
Diffraction Radiation
Monochromator Protocol
osmic mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE Cu FINE FOCUS 1.54 -- --

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 20 98.3 0.103 -- -- 6.6 6607 6468 2.0 2.0 --
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)
2.5 2.59 92.4 0.476 -- 2.3 3.3 175

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 15.0 -- 0.0 -- 6442 307 98.29 -- 0.2067 0.2033 0.2793 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 -- 31 402 0.284 0.44 -- 91.74
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.9698
Anisotropic B[1][1] 0.78
Anisotropic B[1][2] 0.39
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.78
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.17
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.341
r_scbond_it 0.908
r_symmetry_hbond_refined 0.164
r_symmetry_vdw_other 0.277
r_symmetry_vdw_refined 0.224
r_bond_refined_d 0.007
r_bond_other_d 0.003
r_angle_refined_deg 1.553
r_angle_other_deg 1.015
r_chiral_restr 0.05
r_gen_planes_refined 0.004
r_gen_planes_other 0.001
r_nbd_refined 0.124
r_nbd_other 0.23
r_nbtor_refined 0.225
r_nbtor_other 0.066
r_xyhbond_nbd_refined 0.163
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 1266
Heterogen Atoms 27
Solvent Atoms 94

Software

Computing
Computing Package Purpose
PROTEUM PLUS Data Collection
HKL Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMoRE Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 version: 5.2.0019 refinement