7YOF | pdb_00007yof

Crystal Structure of Triple mutant (D67E, A68P, I88L) of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae at 2.3 A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y7L	1Y7L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	278	0.1M HEPES, 1.3M sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
2	41.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.2	α = 90
b = 112.2	β = 90
c = 43.74	γ = 90

Symmetry
Space Group	I 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2014-08-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54179

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.3	40.75	99.98	0.847	66.54	19.1		235300

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.382			0.781	13.29

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1Y7L	2.3	40.75	12294	575	99.951	0.173	0.171	0.17	0.222	0.22	32.432

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-2.135			-2.135		4.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.468
r_dihedral_angle_4_deg	17.321
r_dihedral_angle_3_deg	17.106
r_lrange_it	8.055
r_dihedral_angle_1_deg	5.764
r_scangle_it	5.151
r_mcangle_it	4.338
r_scbond_it	3.49
r_mcbond_it	2.742
r_angle_refined_deg	1.481
r_nbtor_refined	0.305
r_symmetry_nbd_refined	0.244
r_nbd_refined	0.208
r_symmetry_xyhbond_nbd_refined	0.139
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.107
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2319
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing