2GGK | pdb_00002ggk

The mutant A302C of Agrobacterium radiobacter N-carbamoyl-D-amino-acid amidohydrolase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FO6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	lithium sulfate, HEPES buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.091	α = 90
b = 67.819	β = 95.87
c = 138.037	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113	IMAGE PLATE	RIGAKU RAXIS IV		2003-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	30	95.6				56903

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.38	95.3

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-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	1FO6	2.3	30	46601	2459	86.48	0.18	0.18021	0.17816	0.1802	0.21963	0.2011	RANDOM	33.184

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]
2.05		-0.02	0.71		-2.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.686
r_dihedral_angle_4_deg	19.806
r_dihedral_angle_3_deg	15.608
r_dihedral_angle_1_deg	6.745
r_angle_refined_deg	1.315
r_nbtor_refined	0.324
r_symmetry_vdw_refined	0.27
r_symmetry_hbond_refined	0.269
r_nbd_refined	0.231
r_xyhbond_nbd_refined	0.206
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9568
Nucleic Acid Atoms
Solvent Atoms	285
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing