7YOE | pdb_00007yoe

Crystal Structure of A68P single mutant of O-acetyl-L-serine sulfhydrylase from Haemophilus influenzae at 1.88 A

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	278	0.1M HEPES, 1.3M Sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.08	41.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.281	α = 90
b = 112.281	β = 90
c = 43.744	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	293	IMAGE PLATE	MAR scanner 345 mm plate		2012-06-24	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	1.88	39.7	99.64	1	14.75	1.1		22383

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	1.88	1.947	97.48		1	2.01

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	1.88	39.7	22383	1044	99.546	0.202	0.2014	0.2	0.2215	0.22	34.75

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]
-1.922			-1.922		3.845

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.295
r_dihedral_angle_4_deg	17.297
r_dihedral_angle_3_deg	15.945
r_lrange_it	7.547
r_dihedral_angle_1_deg	5.785
r_scangle_it	5.233
r_mcangle_it	4.519
r_scbond_it	3.754
r_mcbond_it	3.085
r_angle_refined_deg	1.571
r_nbtor_refined	0.307
r_nbd_refined	0.212
r_symmetry_nbd_refined	0.209
r_symmetry_xyhbond_nbd_refined	0.197
r_xyhbond_nbd_refined	0.116
r_chiral_restr	0.113
r_bond_refined_d	0.008
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2326
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms

Software

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