X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 290.0
Details sodium citrate, ammonium sulphate, pH 5., VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.9 α = 90
b = 91.3 β = 90
c = 48.4 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
IMAGE PLATE MARRESEARCH -- 2000-05-05
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM30A 0.9795 ESRF BM30A

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
2.4 20 93.0 0.054 0.054 -- 5.7 161039 161039 0.0 0.0 57.01
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)
2.4 2.46 81.0 0.262 0.262 -- 2.7 --

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 2.4 15.0 0.0 0.0 14548 14548 752 96.56 0.20565 0.20565 0.2043 0.23227 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 2.4 2.46 -- 52 1009 0.279 0.245 -- 94.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic after TLS
Mean Isotropic B 36.488
Anisotropic B[1][1] -3.26
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 8.76
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.624
r_scbond_it 3.001
r_bond_refined_d 0.017
r_angle_refined_deg 1.603
r_dihedral_angle_1_deg 3.511
r_dihedral_angle_3_deg 17.338
r_chiral_restr 0.101
r_gen_planes_refined 0.007
r_nbd_refined 0.239
r_xyhbond_nbd_refined 0.157
r_symmetry_vdw_refined 0.11
r_symmetry_hbond_refined 0.077
r_mcbond_it 0.739
r_mcangle_it 1.412
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3705
Luzzati Resolution Cutoff (Low) 15.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1538
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 41

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
SOLVE model building
SCALEPACK data reduction
DENZO data collection