X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Hanging Drop Vapor Batch
Temperature 294.0
Details 10 mg/ml of each protein in 50 mM TrisCl, pH 8.0, 0.05 M NaCl mixed 1:1 with 0.2 M potassium phosphate, pH 4.7, 20% PEG 3350, hanging drop vapor batch, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.42 α = 103.24
b = 48.76 β = 91.29
c = 106.14 γ = 90.18
Symmetry
Space Group P 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 -- 2001-08-01
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL SILICON (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.1 1.0000 ALS 8.2.1

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
2.1 105.41 94.7 -- 0.048 -- 5.4 -- 49303 -- -- --
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)
2.1 2.18 86.5 0.111 0.111 -- 4.9 --

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
-- 2.1 25.0 -- -- -- 46665 2508 95.01 -- 0.1946 0.192 0.234 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 2.1 2.155 -- 167 3327 0.197 0.29 -- 89.61
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.319
Anisotropic B[1][1] -0.82
Anisotropic B[1][2] -0.06
Anisotropic B[1][3] 0.26
Anisotropic B[2][2] 1.7
Anisotropic B[2][3] -0.07
Anisotropic B[3][3] -0.91
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 1.118
r_symmetry_vdw_refined 0.186
r_symmetry_hbond_refined 0.193
r_dihedral_angle_1_deg 6.44
r_nbtor_refined 0.301
r_dihedral_angle_4_deg 14.506
r_xyhbond_nbd_refined 0.192
r_dihedral_angle_2_deg 37.54
r_mcangle_it 1.881
r_scangle_it 4.605
r_bond_refined_d 0.023
r_angle_refined_deg 1.97
r_dihedral_angle_3_deg 16.132
r_nbd_refined 0.214
r_gen_planes_refined 0.01
r_scbond_it 3.061
r_chiral_restr 0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6469
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 372

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 3.006
MAR345dtb data collection
PHASER phasing