X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 394.0
Details 18% PEG 4000, 100 mM Tris, 200 mM ammonium acetate, 3% t-amyl alcohol, 15 % glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 394K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 149.41 α = 90
b = 92.74 β = 130.11
c = 99.13 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 363
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1997-11-01
Diffraction Radiation
Monochromator Protocol
-- single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12B 0.978 NSLS X12B

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
2.5 30 99.3 0.048 -- -- 3.27 117641 116818 1.0 1.0 62.1
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)
2.5 2.54 98.9 -- -- -- -- --

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 2.5 30.0 -- 1.0 35657 33805 1852 99.29 -- 0.20535 0.20322 0.24534 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 2.5 2.565 -- 122 2484 0.238 0.254 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.297
Anisotropic B[1][1] -1.56
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.23
Anisotropic B[2][2] 3.4
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.42
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.261
r_gen_planes_refined 0.005
r_chiral_restr 0.096
r_dihedral_angle_3_deg 16.684
r_dihedral_angle_1_deg 4.239
r_angle_refined_deg 1.52
r_bond_refined_d 0.013
r_xyhbond_nbd_refined 0.19
r_symmetry_vdw_refined 0.237
r_symmetry_hbond_refined 0.214
r_mcbond_it 0.687
r_mcangle_it 1.301
r_scbond_it 1.913
r_scangle_it 3.099
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.412
Luzzati ESD (R-Free Set) 0.265
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5969
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 63

Software

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