X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 277.0
Details Na Acetate, Imidazole, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 195.74 α = 90
b = 195.74 β = 90
c = 80.56 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-05-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 -- ALS 8.3.1

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 72.55 97.3 -- -- -- -- 84753 84733 1.5 1.5 --
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)
2.24 2.36 96.7 -- -- -- -- --

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 2.24 72.55 -- 1.5 84753 78366 4111 97.34 0.231 0.228 0.228 0.276 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 2.24 2.298 -- 304 5750 0.3 0.336 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.785
Anisotropic B[1][1] 2.22
Anisotropic B[1][2] 1.11
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.34
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.233
r_scbond_it 1.375
r_mcangle_it 0.875
r_mcbond_it 0.484
r_symmetry_hbond_refined 0.151
r_symmetry_vdw_other 0.283
r_symmetry_vdw_refined 0.084
r_bond_refined_d 0.013
r_bond_other_d 0.003
r_angle_refined_deg 1.515
r_angle_other_deg 0.98
r_dihedral_angle_1_deg 3.093
r_chiral_restr 0.104
r_gen_planes_refined 0.005
r_gen_planes_other 0.004
r_nbd_refined 0.205
r_nbd_other 0.233
r_nbtor_other 0.084
r_xyhbond_nbd_refined 0.191
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8889
Nucleic Acid Atoms 0
Heterogen Atoms 112
Solvent Atoms 384

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.1.25 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 1.600 data extraction
REFMAC5 version: 5.1.25 refinement
SCALA data processing