X-RAY DIFFRACTION Experimental Data & Validation


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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 = 96.59 α = 90
b = 96.59 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 -- 2002-02-22
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
1.96 83.7 97.6 0.057 0.057 -- 3.9 -- 29990 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)
1.96 2.07 99.2 0.369 0.369 2.0 3.5 --

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 2.0 83.65 -- 1.5 0 27652 1459 97.61 0.219 0.218 0.218 0.251 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 2.0 2.031 -- 112 2028 0.315 0.363 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.056
Anisotropic B[1][1] 1.21
Anisotropic B[1][2] 0.6
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.81
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.625
r_scbond_it 1.601
r_mcangle_it 1.076
r_mcbond_it 0.594
r_symmetry_hbond_refined 0.111
r_symmetry_vdw_other 0.307
r_symmetry_vdw_refined 0.132
r_bond_refined_d 0.012
r_bond_other_d 0.002
r_angle_refined_deg 1.623
r_angle_other_deg 0.826
r_dihedral_angle_1_deg 3.089
r_chiral_restr 0.085
r_gen_planes_refined 0.005
r_gen_planes_other 0.004
r_nbd_refined 0.202
r_nbd_other 0.235
r_nbtor_other 0.08
r_xyhbond_nbd_refined 0.149
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2230
Nucleic Acid Atoms 0
Heterogen Atoms 23
Solvent Atoms 105

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