X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Under Oil Microbatch
pH 5.5
Temperature 277.0
Details Bis-Tris, Sodium Chloride, PEG 3350, Xylitol, pH 5.5, under oil microbatch, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.77 α = 90
b = 95.39 β = 90
c = 113.69 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD -- -- 2007-03-17
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID

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
2.2 50 99.9 0.049 -- -- 6.7 -- 37593 -- -- --
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)
2.2 2.28 100.0 0.271 -- -- 6.3 --

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 2.2 32.06 -- -- -- 35675 1876 99.91 -- 0.22079 0.21894 0.25515 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 2.2 2.257 -- 139 2557 0.314 0.418 -- 99.93
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.695
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.02
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.638
r_scbond_it 1.734
r_mcangle_it 1.366
r_mcbond_it 0.81
r_nbd_refined 0.215
r_gen_planes_refined 0.009
r_chiral_restr 0.114
r_dihedral_angle_4_deg 21.281
r_dihedral_angle_3_deg 19.007
r_dihedral_angle_2_deg 36.037
r_dihedral_angle_1_deg 8.804
r_angle_refined_deg 1.635
r_bond_refined_d 0.015
r_nbtor_refined 0.303
r_xyhbond_nbd_refined 0.152
r_symmetry_vdw_refined 0.236
r_symmetry_hbond_refined 0.041
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3290
Nucleic Acid Atoms 609
Heterogen Atoms 48
Solvent Atoms 134

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
pdb_extract version: 3.004 data extraction
REFMAC5 version: 5.3.0020 refinement
Phaser molecular replacement
HKL data processing