X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.8
Temperature 277.0
Details 22.5% PEG MME 200, 0.1M Bicine pH 7.8, VAPOR DIFFUSION, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 122.84 α = 90
b = 122.77 β = 114.68
c = 145.11 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.3 1.0000 ALS 5.0.3

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
2.69 50 99.9 0.095 -- -- 4.0 -- 108584 -- -- --
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)
2.69 2.75 100.0 0.608 -- -- 3.8 7174

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 2.69 50.0 -- 0.0 -- 108370 5412 99.15 -- 0.198 0.195 0.248 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 2.69 2.76 -- 372 7007 0.324 0.428 -- 91.64
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 48.26
Anisotropic B[1][1] -3.41
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.58
Anisotropic B[2][2] 4.37
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.45
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.132
r_dihedral_angle_2_deg 33.599
r_nbtor_refined 0.313
r_nbd_refined 0.2
r_dihedral_angle_3_deg 16.767
r_dihedral_angle_1_deg 5.22
r_xyhbond_nbd_refined 0.133
r_gen_planes_refined 0.003
r_angle_refined_deg 1.258
r_chiral_restr 0.091
r_scbond_it 0.996
r_bond_refined_d 0.009
r_dihedral_angle_4_deg 17.998
r_scangle_it 1.666
r_symmetry_vdw_refined 0.185
r_mcbond_it 0.404
r_mcangle_it 0.722
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 23743
Nucleic Acid Atoms 0
Heterogen Atoms 416
Solvent Atoms 774

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 3.006
ADSC data collection version: QUANTUM
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing