X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details PEG 8000, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.77 α = 90
b = 126.02 β = 91.06
c = 132.29 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH premirror, triangular monochromator, bent mirror 2001-11-03
Diffraction Radiation
Monochromator Protocol
triangular MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8459, 0.9779, 0.9783, 0.9392 EMBL/DESY, HAMBURG BW7B

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 40 95.6 0.055 -- -- -- 220969 220969 0.0 0.0 --
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 1.97 95.8 0.21 -- -- -- --

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
MAD 1.9 40.0 -- 0.0 209646 209646 11118 95.53 0.15027 0.15027 0.1488 0.17802 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 -- 848 15490 0.211 0.242 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.796
Anisotropic B[1][1] -0.57
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.13
Anisotropic B[2][2] -0.47
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.03
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.084
r_nbd_other 0.221
r_nbd_refined 0.181
r_gen_planes_other 0.001
r_gen_planes_refined 0.003
r_chiral_restr 0.099
r_dihedral_angle_1_deg 2.712
r_angle_other_deg 0.713
r_angle_refined_deg 1.143
r_bond_other_d 0.006
r_bond_refined_d 0.013
r_xyhbond_nbd_refined 0.158
r_metal_ion_refined 0.103
r_symmetry_vdw_refined 0.079
r_symmetry_vdw_other 0.22
r_symmetry_hbond_refined 0.122
r_mcbond_it 1.552
r_mcangle_it 2.377
r_scbond_it 3.721
r_scangle_it 5.463
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19392
Nucleic Acid Atoms 0
Heterogen Atoms 64
Solvent Atoms 2246

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHAKE-N-BAKE VRSION 2.1, SOLVE, RESOLVE, ARP/WARP Structure Solution
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.19 refinement
ARP/wARP model building
SOLVE/RESOLVE model building
SnB2.1 model building
SCALEPACK data reduction
DENZO data collection