X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.3
Temperature 295.0
Details potassium phosphate buffer, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.55 α = 90
b = 60.67 β = 90
c = 89.09 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH Mirrors 2003-03-04
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 5ID-B 0.97014 APS 5ID-B

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
1.45 50 99.6 0.06 -- -- 4.9 40724 40562 -- 3.0 --
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)
1.45 1.53 99.8 0.444 -- 1.6 3.5 20643

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 1.45 50.0 0.0 0.0 40562 38464 2025 99.46 -- 0.20313 0.20091 0.24487 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 1.45 1.488 5834 146 2801 0.265 0.31 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.786
Anisotropic B[1][1] -0.77
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.85
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.08
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.512
r_scbond_it 2.881
r_mcangle_it 1.885
r_mcbond_it 1.126
r_symmetry_vdw_refined 0.388
r_nbd_refined 0.325
r_gen_planes_refined 0.009
r_chiral_restr 0.127
r_dihedral_angle_1_deg 5.938
r_angle_refined_deg 1.864
r_bond_refined_d 0.018
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.083
Luzzati ESD (R-Free Set) 0.089
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2030
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 227

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
REFMAC 5.1 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1 refinement
AMoRE model building
SCALA data reduction
MOSFLM data collection