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 PEG 400, bicine, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.5 α = 90
b = 102.5 β = 90
c = 156.5 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 190
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 1999-12-07
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 1.000 ALS 5.0.2

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
3 30 99.5 0.103 -- -- 13.2 -- 26440 -- 1.0 --
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)
3.0 3.05 100.0 0.51 -- 1.7 -- --

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 3.0 30.0 -- 0.0 26614 22595 1223 89.6 0.2595 0.24447 0.24215 0.28663 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 3.0 3.077 -- 93 1531 0.279 0.393 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.64
Anisotropic B[1][1] 4.4
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.37
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.336
r_gen_planes_refined 0.012
r_chiral_restr 0.24
r_dihedral_angle_1_deg 12.597
r_angle_refined_deg 3.562
r_bond_refined_d 0.043
r_xyhbond_nbd_refined 0.241
r_symmetry_vdw_refined 0.748
r_symmetry_hbond_refined 0.57
r_mcbond_it 1.318
r_mcangle_it 2.47
r_scbond_it 4.183
r_scangle_it 6.983
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.46
Luzzati Sigma A (Observed) 0.64
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.53
Luzzati Sigma A (R-Free Set) 0.67
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3774
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 56

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5.1 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1 refinement
CNS model building
SCALEPACK data reduction
DENZO data collection