7YOK | pdb_00007yok

Crystal Structure of Tetra mutant (D67E, A68P, L98I, A301S) tetra mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae at 2.8 A

X-RAY DIFFRACTION

---

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
2.14	42.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.043	α = 90
b = 113.043	β = 90
c = 44.343	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		2012-09-11	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	2.8	39.97	87.33	1	31.05	1.1		6815

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	2.802	2.902			1	12.88

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	2.799	39.97	6194	294	87.154	0.23	0.2286	0.23	0.265	0.27	75.712

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]
-7.107			-7.107		14.213

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.682
r_lrange_it	19.185
r_dihedral_angle_3_deg	16.897
r_dihedral_angle_4_deg	15.026
r_scangle_it	13.127
r_mcangle_it	11.922
r_scbond_it	9.022
r_mcbond_it	7.801
r_dihedral_angle_1_deg	6.242
r_angle_refined_deg	1.505
r_symmetry_nbd_refined	0.318
r_nbtor_refined	0.308
r_symmetry_xyhbond_nbd_refined	0.243
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.115
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2286
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling
PHASER	phasing