X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5
Details PROTEIN WAS CRYSTALLIZED FROM 15% PEG 6000, 100 MM SODIUM CITRATE, PH 5.0 AND 8% PEG 400 AT 20 DEGREES C.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.05 α = 90
b = 108.05 β = 90
c = 117.7 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC RH-COATED SI MIRROR 2002-10-07
Diffraction Radiation
Monochromator Protocol
BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATER SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE F1 -- CHESS F1

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
4 26 98.0 0.08 -- -- 4.5 -- 100402 -- 0.0 141.1
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)
4.0 4.09 94.3 0.82 -- 1.3 4.0 --

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
MIRAS 4.0 26.0 -- -- -- 5842 279 98.0 -- 0.385 0.385 0.388 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 4.0 4.37 -- 67 1309 0.403 0.533 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 128.8
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.03
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.341
r_gen_planes_refined 0.005
r_chiral_restr 0.112
r_dihedral_angle_4_deg 18.61
r_dihedral_angle_3_deg 24.209
r_dihedral_angle_2_deg 45.267
r_dihedral_angle_1_deg 8.116
r_angle_refined_deg 2.067
r_bond_refined_d 0.014
r_nbtor_refined 0.344
r_xyhbond_nbd_refined 0.268
r_symmetry_vdw_refined 0.368
r_symmetry_hbond_refined 0.194
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2471
Nucleic Acid Atoms 0
Heterogen Atoms 615
Solvent Atoms 0

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE, SHARP Structure Solution
REFMAC 5.2.0003 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0003 refinement
SHARP model building
SOLVE model building