X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 277.0
Details PEG4000, MgCl2, pH 8.5, vapor diffusion, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.87 α = 90
b = 42.87 β = 90
c = 231.49 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD -- -- 2008-02-27
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 -- NSLS X25

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 50 98.8 0.055 -- -- 4.4 -- 23986 -- -- --
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 92.2 0.108 -- -- 4.3 2248

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
-- 2.11 37.48 -- 0.0 -- 23906 1221 99.5 -- 0.17 0.167 0.229 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 2.106 2.161 -- 85 1697 0.168 0.221 -- 98.02
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.907
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.615
r_scbond_it 3.276
r_mcangle_it 1.907
r_mcbond_it 1.367
r_symmetry_hbond_refined 0.205
r_bond_refined_d 0.022
r_angle_refined_deg 2.268
r_dihedral_angle_1_deg 31.619
r_dihedral_angle_2_deg 37.066
r_dihedral_angle_3_deg 18.257
r_dihedral_angle_4_deg 17.13
r_chiral_restr 0.185
r_gen_planes_refined 0.009
r_nbd_refined 0.216
r_nbtor_refined 0.311
r_xyhbond_nbd_refined 0.178
r_symmetry_vdw_refined 0.328
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3692
Nucleic Acid Atoms 0
Heterogen Atoms 150
Solvent Atoms 190

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.006 data extraction
REFMAC5 version: 5.2.0019 refinement
HKL data processing