1VKN | pdb_00001vkn

Crystal structure of N-acetyl-gamma-glutamyl-phosphate reductase (TM1782) from Thermotoga maritima at 1.80 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP		295	13.50% PEG 3350, 0.50M (NH4)formate , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 295K
2	VAPOR DIFFUSION,SITTING DROP,NANODROP		295	13.50M (NH4)formate, 0.50% PEG 3350 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.17
2.31	46.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.098	α = 90
b = 92.103	β = 112.76
c = 100.88	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	100	CCD	ADSC		2003-09-20	M	MAD
2	1	100

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1		ALS	8.2.1
2	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.9794, 0.9795, 1.0000	ALS	8.2.1

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	1.8	50	99.46	0.055	18.91	3.96		131126			37.18

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	1.8	1.84	95.79		0.507	2.12	2.85	8413

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.8	46.51	124606	6565	98.12	0.17942	0.17766	0.19	0.21182	0.22	RANDOM	34.956

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]
3.68		3.77	-1.52		0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.361
r_dihedral_angle_4_deg	19.618
r_dihedral_angle_3_deg	14.159
r_scangle_it	7.14
r_dihedral_angle_1_deg	6.477
r_scbond_it	5.286
r_mcangle_it	3.248
r_mcbond_it	2.384
r_angle_refined_deg	1.515
r_angle_other_deg	0.844
r_mcbond_other	0.651
r_symmetry_vdw_other	0.237
r_nbd_refined	0.207
r_nbd_other	0.181
r_xyhbond_nbd_refined	0.149
r_symmetry_hbond_refined	0.144
r_symmetry_vdw_refined	0.096
r_chiral_restr	0.092
r_nbtor_other	0.084
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10513
Nucleic Acid Atoms
Solvent Atoms	756
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
autoSHARP	phasing
REFMAC	refinement