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, Ammonium Sulfate, PEG 3350, Ethylene Glycol, pH 5.5, under oil microbatch, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.15 α = 90
b = 98.87 β = 90
c = 126.31 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD -- -- 2006-10-30
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 0.97934 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 94.8 0.066 -- -- 5.5 -- 36557 -- -- --
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 71.3 0.345 -- -- 5.0 2689

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 2.21 39.87 -- 0.0 -- 36498 1819 94.4 -- 0.211 0.208 0.257 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 2.21 2.264 -- 84 1820 0.267 0.307 -- 67.37
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.242
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.16
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.695
r_scbond_it 1.931
r_mcangle_it 1.487
r_mcbond_it 0.866
r_symmetry_hbond_refined 0.28
r_bond_refined_d 0.018
r_angle_refined_deg 1.795
r_dihedral_angle_1_deg 6.699
r_dihedral_angle_2_deg 36.209
r_dihedral_angle_3_deg 19.6
r_dihedral_angle_4_deg 17.293
r_chiral_restr 0.122
r_gen_planes_refined 0.007
r_nbd_refined 0.208
r_nbtor_refined 0.306
r_xyhbond_nbd_refined 0.167
r_symmetry_vdw_refined 0.224
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3527
Nucleic Acid Atoms 609
Heterogen Atoms 40
Solvent Atoms 131

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 5.3.0020 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