X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details PEG 4000, sodium acetate, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.8 α = 90
b = 49.7 β = 98.4
c = 60.5 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 105
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2001-08-30
Diffraction Radiation
Monochromator Protocol
Si Channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM1A 0.8727 ESRF BM1A

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
1.63 15 95.36 -- 0.04 -- 3.65 38783 38783 -- 0.0 22.1
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)
1.63 1.69 67.3 -- 0.433 2.1 2.5 2775

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
SIRAS 1.63 15.0 -- 0.0 38477 36564 1913 95.36 0.2018 0.2018 0.20067 0.22277 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 1.63 1.672 -- 112 2276 0.26 0.297 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.739
Anisotropic B[1][1] 1.33
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.61
Anisotropic B[2][2] -0.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.39
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.197
r_dihedral_angle_1_deg 3.298
r_nbd_refined 0.241
r_dihedral_angle_3_deg 13.132
r_chiral_restr 0.068
r_bond_other_d 0.001
r_mcangle_it 1.35
r_scangle_it 3.429
r_symmetry_vdw_other 0.254
r_nbd_other 0.193
r_xyhbond_nbd_other 0.06
r_scbond_it 2.086
r_symmetry_hbond_refined 0.153
r_angle_other_deg 0.651
r_angle_refined_deg 1.135
r_gen_planes_other 0.002
r_bond_refined_d 0.009
r_symmetry_vdw_refined 0.198
r_gen_planes_refined 0.004
r_mcbond_it 0.694
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2066
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 419

Software

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