Mass: 18.015 Da / Num. of mol.: 1109 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 6.5 - 8.0% PEG4000, protein at 40 mg/mL in 50 mM TrisCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution: 2.2→2.28 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.131 / % possible all: 82.8
Reflection
*PLUS
Num. measured all: 296455 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 82.8 % / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 4.2
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Processing
Software
Name
Version
Classification
X-PLOR
modelbuilding
X-PLOR
3.851
refinement
DENZO
datareduction
SCALEPACK
datascaling
X-PLOR
phasing
Refinement
Resolution: 2.2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: BOND ANGLES AND LENGTHS TO THE HEME IRON FROM BOTH THE TYR358 LIGAND AND THE HEME NITROGENS WERE UNCONSTRAINED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.227
12276
10 %
Random
Rwork
0.172
-
-
-
all
0.176
123016
-
-
obs
0.176
123184
-
-
Displacement parameters
Biso mean: 62.92 Å2
Baniso -1
Baniso -2
Baniso -3
1-
5.5339 Å2
0 Å2
0 Å2
2-
-
-1.5138 Å2
0 Å2
3-
-
-
-4.0201 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
16066
0
268
1109
17443
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
x_bond_d
0.007
X-RAY DIFFRACTION
x_angle_deg
1.3
X-RAY DIFFRACTION
x_mcbond_it
0.416
1.5
X-RAY DIFFRACTION
x_mcangle_it
0.755
2
X-RAY DIFFRACTION
x_scbond_it
0.496
2
X-RAY DIFFRACTION
x_scangle_it
0.82
2.5
LS refinement shell
Resolution: 2.2→2.3 Å / Total num. of bins used: 8
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