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 = 41.89 α = 90
b = 61.04 β = 90
c = 88.68 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
1.9 20 98.9 0.079 -- -- 5.5 18277 17299 -- 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)
1.9 2.09 99.7 0.236 -- 3.5 5.5 4299

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 1.9 20.0 0.0 0.0 18277 17299 937 98.47 -- 0.1934 0.19054 0.24697 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 1.9 1.949 1239 74 1239 0.188 0.246 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.196
Anisotropic B[1][1] -0.97
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.41
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.44
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.089
r_scbond_it 3.461
r_mcangle_it 1.754
r_mcbond_it 1.044
r_symmetry_vdw_refined 0.359
r_nbd_refined 0.313
r_gen_planes_refined 0.009
r_chiral_restr 0.134
r_dihedral_angle_1_deg 6.04
r_angle_refined_deg 1.938
r_bond_refined_d 0.023
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.193
Luzzati ESD (R-Free Set) 0.173
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2026
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 180

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: 5.1.80 refinement
AMoRE model building
SCALA data reduction
MOSFLM data collection