X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 298.0
Details 8.5% PEG 4000, 8.5% MPD, 100 mM Na Citrate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 71.74 α = 90
b = 88.2 β = 90
c = 197.55 γ = 90
Symmetry
Space Group P 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 225 mm -- 2003-02-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID -- APS 22-ID

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 50 95.6 0.108 -- -- 5.3 85338 81583 -- -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)
2.0 2.07 85.9 0.496 -- -- 2.6 --

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 2.0 44.11 -- -- 85416 74341 3926 91.63 -- 0.20513 0.20314 0.24284 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 2.0 2.052 -- 232 4429 0.238 0.27 -- 74.85
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.779
Anisotropic B[1][1] -0.03
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.06
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.014
r_scbond_it 0.627
r_mcangle_it 1.083
r_mcbond_it 0.655
r_nbd_refined 0.208
r_gen_planes_refined 0.003
r_chiral_restr 0.062
r_dihedral_angle_4_deg 19.426
r_dihedral_angle_3_deg 13.938
r_dihedral_angle_2_deg 33.804
r_dihedral_angle_1_deg 5.198
r_angle_refined_deg 0.962
r_bond_refined_d 0.006
r_nbtor_refined 0.318
r_xyhbond_nbd_refined 0.206
r_symmetry_vdw_refined 0.175
r_symmetry_hbond_refined 0.182
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7096
Nucleic Acid Atoms 0
Heterogen Atoms 205
Solvent Atoms 665

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 2.000 data extraction
REFMAC5 version: 5.2.0005 refinement
HKL data processing