X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 277.0
Details 0.2000M NH4H2PO4, 20.0000% PEG-3350, No Buffer pH 4.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.63 α = 90
b = 97.75 β = 90
c = 114.01 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2009-02-22
Diffraction Radiation
Monochromator Protocol
Single crystal Si(111) bent monochromator (horizontal focusing) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.91162,0.97889 SSRL BL11-1

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
1.75 29.71 99.6 0.077 0.077 -- 3.7 -- 54325 -- -- 19.443
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)
1.75 1.8 99.0 0.435 0.435 1.8 3.7 3900

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 1.75 29.709 -- 0.0 -- 54272 2759 99.54 -- 0.172 0.17 0.21 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 1.75 1.795 -- 199 3698 0.215 0.258 -- 98.86
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.703
Anisotropic B[1][1] 0.19
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.54
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 15.019
r_mcbond_it 2.001
r_chiral_restr 0.087
r_scangle_it 7.134
r_bond_refined_d 0.017
r_angle_other_deg 0.929
r_mcbond_other 0.575
r_bond_other_d 0.001
r_gen_planes_other 0.002
r_scbond_it 4.853
r_dihedral_angle_3_deg 13.382
r_dihedral_angle_1_deg 5.667
r_dihedral_angle_2_deg 36.897
r_gen_planes_refined 0.008
r_angle_refined_deg 1.506
r_mcangle_it 3.251
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4325
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 594

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0053
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
SCALA data scaling version: 3.2.5
PDB_EXTRACT data extraction version: 3.006
MOSFLM data reduction
SHELXD phasing
autoSHARP phasing