4CQC | pdb_00004cqc

The reaction mechanism of the N-isopropylammelide isopropylaminohydrolase AtzC: insights from structural and mutagenesis studies

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QT3	PDB ENTRY 2QT3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		PROTEIN AT 5.5 MG/ML OVER A RESERVOIR OF 2.5 M MALONATE PH 7.0, 100 MM HEPES BUFFER AT PH 7.5; DROPS WERE 150 NL PLUS 150 NL. IN-SITU THROMBIN TREATMENT WAS USED TO REMOVE THE HIS-TAG.

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.234	α = 90
b = 87.28	β = 103.93
c = 114.364	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC CCD		2013-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2		Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.2	46.3	99.4	0.14	12.5	7.7		51202

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	98.9		0.8	2.8	7.7

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 (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	PDB ENTRY 2QT3	2.2	46.37	48598	2603	99.21	0.19695	0.19556	0.2	0.22311	0.23	RANDOM	32.228

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]
2.59		0.43	-2.77		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.21
r_dihedral_angle_4_deg	16.852
r_dihedral_angle_3_deg	13.926
r_dihedral_angle_1_deg	5.916
r_mcangle_it	3.321
r_scbond_it	3.127
r_mcbond_it	2.338
r_mcbond_other	2.338
r_angle_refined_deg	1.269
r_angle_other_deg	0.824
r_chiral_restr	0.074
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6275
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	34

Software

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