X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch
pH 5.5
Temperature 298.0
Details PEG 3000, Sodium Citrate, Magnesium Chloride, AMP-PNP, pH 5.5, Microbatch, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 146.65 α = 90
b = 219.19 β = 90
c = 106.92 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-01-31
Diffraction Radiation
Monochromator Protocol
Double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.1 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
2.3 20 98.1 -- 0.111 -- -- 153022 150115 4.1 4.1 --
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)
2.3 2.38 88.7 -- 0.413 2.24 -- 13432

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
MAD 2.3 20.0 -- 0.0 150115 137434 12535 98.1 0.21854 0.21854 0.21447 0.26327 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 2.3 2.359 -- 791 8944 0.257 0.307 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.95
Anisotropic B[1][1] 0.31
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.55
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.86
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.272
r_gen_planes_refined 0.006
r_chiral_restr 0.105
r_dihedral_angle_3_deg 18.603
r_dihedral_angle_1_deg 4.249
r_angle_refined_deg 1.424
r_bond_refined_d 0.013
r_xyhbond_nbd_refined 0.169
r_symmetry_vdw_refined 0.291
r_symmetry_hbond_refined 0.272
r_mcbond_it 0.735
r_mcangle_it 1.397
r_scbond_it 2.317
r_scangle_it 3.849
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 22053
Nucleic Acid Atoms 0
Heterogen Atoms 193
Solvent Atoms 811

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHARP Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
SHARP model building
SCALEPACK data reduction
DENZO data collection