X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 300.0
Details pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.23 α = 90
b = 59.54 β = 82.22
c = 59.86 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Yale Mirrors 2007-08-17
Diffraction Radiation
Monochromator Protocol
Yale Mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

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
2.1 50 95.8 0.069 -- -- 3.0 56701 20006 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)
2.1 2.18 90.1 0.493 -- -- -- 1867

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
-- 2.1 40.0 -- 0.0 -- 20000 1016 95.79 -- 0.183 0.179 0.249 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 2.1 2.158 -- 73 1284 0.264 0.352 -- 88.63
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.666
Anisotropic B[1][1] -2.13
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.25
Anisotropic B[2][2] 1.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.02
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 1.585
r_nbd_other 0.202
r_mcbond_it 0.888
r_bond_other_d 0.002
r_dihedral_angle_3_deg 15.567
r_dihedral_angle_4_deg 20.246
r_mcangle_it 1.068
r_scangle_it 2.274
r_symmetry_hbond_refined 0.215
r_xyhbond_nbd_refined 0.182
r_chiral_restr 0.08
r_angle_other_deg 0.719
r_gen_planes_other 0.002
r_mcbond_other 0.164
r_dihedral_angle_1_deg 7.243
r_angle_refined_deg 1.413
r_dihedral_angle_2_deg 38.71
r_gen_planes_refined 0.006
r_nbtor_other 0.087
r_symmetry_vdw_other 0.248
r_nbd_refined 0.189
r_symmetry_vdw_refined 0.198
r_nbtor_refined 0.174
r_bond_refined_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2937
Nucleic Acid Atoms 0
Heterogen Atoms 137
Solvent Atoms 156

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement version: 5.2.0005
PDB_EXTRACT data extraction version: 3.006
AMoRE phasing