X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.0
Details 4.25 M NaNitrate, 0.1 M Bis-Tris, 10 mM NAD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 120.94 α = 90
b = 120.94 β = 90
c = 91.79 γ = 120
Symmetry
Space Group P 3 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD MIRROR 2010-07-31
Diffraction Radiation
Monochromator Protocol
SI-111 CHANNEl MOLECULAR REPLACEMENT
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G

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
2.74 30 100.0 0.076 -- -- 7.6 20690 20690 -- -3.0 74.0
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)
2.74 2.8 100.0 0.882 -- 2.3 7.7 1029

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 2.74 30.0 -- 0.0 19563 19563 1056 99.21 -- 0.21084 0.20911 0.24451 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 2.74 2.811 -- 75 1392 0.298 0.342 -- 95.51
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 72.083
Anisotropic B[1][1] 1.27
Anisotropic B[1][2] 0.64
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.27
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.91
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.016
r_angle_refined_deg 1.653
r_dihedral_angle_2_deg 35.761
r_dihedral_angle_3_deg 19.143
r_dihedral_angle_1_deg 5.218
r_mcangle_it 1.475
r_gen_planes_refined 0.005
r_scbond_it 2.97
r_mcbond_it 0.72
r_dihedral_angle_4_deg 20.196
r_scangle_it 4.636
r_chiral_restr 0.11
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.4
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3577
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 65

Software

Software
Software Name Purpose
Blu-Ice data collection version: Max
PHENIX model building
CCP4 model building
MrBUMP phasing
REFMAC refinement version: 5.5.0109
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing
CCP4 phasing