7HK5 | pdb_00007hk5

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	8-21 mg/ml protein in 20mM HEPES/NaOH pH 7.4, 0.1 M NaCl, 100 mM MgCl2, 30mM NH4Cl mixed 1+1 with 0.2 M Ammonium acetate, 0.1 M Bis-Tris/HCl pH 5.5, 25 %w/v PEG 3350, 3 %v/v TMAO

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 219.38	α = 90
b = 219.38	β = 90
c = 135	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		2016-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1	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	2.07	49.6	99.9	0.284	0.294	0.996	7.79	14.109		198488			33.86

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	2.07	2.12	100		3.965	4.11	0.323	0.84	14.403

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	2.07	49.6	1.33	198213	9818	99.82	0.1838	0.1816	0.1877	0.2246	0.2306	RANDOM	40.259

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	15.342
f_angle_d	0.994
f_chiral_restr	0.059
f_bond_d	0.01
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19531
Nucleic Acid Atoms
Solvent Atoms	1608
Heterogen Atoms	34

Software

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