X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 290.0
Details BrmeB.00183.a.B1.PS01877 at 20.3 mg/mL, RigakuReagents JCSG+ screen, h8: 25% PEG3350, 200 mM sodium chloride, 100 mM Bis-Tris-HCl, pH 5.5, cryoprotection: 15% ethylene glycol in two steps, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.45 α = 90
b = 88.45 β = 90
c = 142.68 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2013-12-22
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 1.0000 ALS 5.0.2

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
1.5 50 99.5 0.044 -- -- 3.6 100819 100352 0.0 -3.0 23.829
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)
1.5 1.54 99.2 0.39 -- 2.43 -- --

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 1.5 50.0 -- 0.0 100819 100315 4848 99.54 0.1559 0.1559 0.1546 0.1826 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 1.5 1.539 7073 307 7073 0.222 0.212 -- 99.21
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC, TLS
Mean Isotropic B 19.044
Anisotropic B[1][1] -0.4
Anisotropic B[1][2] -0.2
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.4
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.28
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.001
r_mcbond_it 0.869
r_chiral_restr 0.094
r_mcbond_other 0.856
r_dihedral_angle_1_deg 5.755
r_angle_other_deg 0.859
r_gen_planes_other 0.004
r_dihedral_angle_2_deg 36.101
r_dihedral_angle_4_deg 19.553
r_bond_refined_d 0.011
r_mcangle_it 1.409
r_dihedral_angle_3_deg 12.072
r_gen_planes_refined 0.009
r_angle_refined_deg 1.556
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4556
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 711

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 2.5.5
REFMAC refinement version: 5.8.0049
PDB_EXTRACT data extraction version: 3.14
BOS data collection
XDS data reduction