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_symmetry_vdw_other 0.277
r_scangle_it 1.341
r_chiral_restr 0.05
r_angle_refined_deg 1.553
r_angle_other_deg 1.015
r_nbtor_other 0.066
r_gen_planes_refined 0.004
r_symmetry_hbond_refined 0.164
r_bond_refined_d 0.007
r_bond_other_d 0.003
r_nbd_refined 0.124
r_gen_planes_other 0.001
r_nbd_other 0.23
r_nbtor_refined 0.225
r_scbond_it 0.908
r_xyhbond_nbd_refined 0.163
r_symmetry_vdw_refined 0.224
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

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.10
PROTEUM PLUS data collection version: PLUS
HKL data reduction
SCALEPACK data scaling
AMoRE phasing