7HK6 | pdb_00007hk6

Crystal Structure of N-methylhydantoinase in complex with 1-methylimidazolidine-2,4-dione, iodide soak

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	9.4 mg/ml protein in 20mM HEPES/NaOH pH 7.4, 0.1 M NaCl, 100 mM MgCl2, 30mM NH4Cl mixed 1+1 with 0.1 M Bis-Tris/HCl pH 5.5, 25% PEG 3350, 0.2 M ammonium sulfate, 3 %w/v TMAO, 5 %w/v DDM

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 217.79	α = 90
b = 217.79	β = 90
c = 133.42	γ = 90

Symmetry
Space Group	P 42 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	PSI PILATUS 6M		2016-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.770030	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.62	49.12	100	0.334	0.346	0.994	8.27	14.566		96326			52.95

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.62	2.69	100		3.43	3.554	0.354	0.79	14.638

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	inhouse model	2.62	49.121	1.34	96196	4702	99.93	0.1846	0.1821	0.186	0.2329	0.2353	RANDOM	53.7913

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.357
f_angle_d	0.998
f_chiral_restr	0.058
f_bond_d	0.008
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19531
Nucleic Acid Atoms
Solvent Atoms	373
Heterogen Atoms	73

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing