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_dihedral_angle_3_deg 19.007
r_nbtor_refined 0.303
r_scangle_it 2.638
r_gen_planes_refined 0.009
r_symmetry_vdw_refined 0.236
r_dihedral_angle_1_deg 8.804
r_xyhbond_nbd_refined 0.152
r_scbond_it 1.734
r_dihedral_angle_4_deg 21.281
r_angle_refined_deg 1.635
r_nbd_refined 0.215
r_chiral_restr 0.114
r_mcbond_it 0.81
r_dihedral_angle_2_deg 36.037
r_bond_refined_d 0.015
r_mcangle_it 1.366
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

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement version: 5.3.0020
PDB_EXTRACT data extraction version: 3.004
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling