X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 298.0
Details 0.2M AMMONIUM ACETATE, 0.1M BIS:TRIS:HCL, PH 6.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.18 α = 90
b = 81.22 β = 98.17
c = 82.95 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 315 -- 2013-03-28
Diffraction Radiation
Monochromator Protocol
-- single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A

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
1.49 50 91.6 0.073 -- -- 3.0 -- 100585 -- -- --
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)
1.49 1.52 58.2 0.556 -- -- 2.6 --

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 1.5 40.12 -- -- -- 94208 4984 92.46 -- 0.16012 0.15857 0.18974 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 1.5 1.539 -- 247 4733 0.254 0.294 -- 63.72
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.79
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.71
Anisotropic B[2][2] -0.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.15
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 11.506
r_sphericity_free 26.024
r_rigid_bond_restr 3.073
r_gen_planes_refined 0.005
r_chiral_restr 0.077
r_dihedral_angle_4_deg 14.288
r_dihedral_angle_3_deg 12.905
r_dihedral_angle_2_deg 37.073
r_dihedral_angle_1_deg 5.349
r_angle_refined_deg 1.161
r_bond_refined_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5008
Nucleic Acid Atoms 0
Heterogen Atoms 82
Solvent Atoms 552

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
Phaser molecular replacement
SCALEPACK data reduction