X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 295.0
Details 20 mM glutamic acid (racemic), 20 mM glycine, 20 mM serine (racemic), 20 mM alanine (racemic), 20 mM lysine-HCl (racemic), 50 mM MOPS, 50 mM Sodium HEPES, pH 7.5; 20% Ethylene Glycol, 10% PEG 8000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 95.29 α = 90
b = 152.35 β = 92.19
c = 149.9 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
PIXEL DECTRIS PILATUS 6M -- 2015-01-31
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1

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
1.95 48.1 99.8 0.092 -- -- 6.84 -- 310836 -- -- 37.0
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)
1.95 2.06 98.9 -- -- 1.98 -- --

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 2.05 48.1 -- -- -- 253577 13347 99.94 -- 0.17021 0.16838 0.2054 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 2.05 2.103 -- 982 18671 0.236 0.262 -- 99.98
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.134
Anisotropic B[1][1] 2.47
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.04
Anisotropic B[2][2] -2.5
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.12
RMS Deviations
Key Refinement Restraint Deviation
r_long_range_B_other 6.061
r_mcbond_other 0.439
r_mcangle_it 0.753
r_scangle_other 1.163
r_mcangle_other 0.753
r_angle_other_deg 1.03
r_bond_refined_d 0.016
r_angle_refined_deg 1.748
r_scbond_other 0.722
r_mcbond_it 0.439
r_long_range_B_refined 6.092
r_chiral_restr 0.103
r_dihedral_angle_1_deg 6.314
r_bond_other_d 0.002
r_gen_planes_other 0.002
r_dihedral_angle_4_deg 19.735
r_scbond_it 0.73
r_gen_planes_refined 0.008
r_dihedral_angle_2_deg 36.763
r_dihedral_angle_3_deg 13.529
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 30004
Nucleic Acid Atoms 0
Heterogen Atoms 186
Solvent Atoms 1353

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0135
XDS data reduction version: November 3, 2014
BALBES phasing version: 1.0.0.Nov_16_2011
XDS data scaling