2IHT | pdb_00002iht

Carboxyethylarginine synthase from Streptomyces clavuligerus: SeMet structure

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	290	1.6 M (NH4)2SO4, 0.1 M HEPES pH 7.4, 10 mg/mL protein with 3-fold excess of ThDP, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.882	α = 90
b = 127.279	β = 90
c = 197.328	γ = 90

Symmetry
Space Group	P 21 21 21

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 QUANTUM 4		2003-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.1	1.488	SRS	PX14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	42.258	96.3	0.075	0.075	6.6	3.8	199701	192312			15.676

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	79.6		0.181	0.181	1.9	2.8	22759

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 1UPA	2	42.258	199913	192236	9261	96.16	0.154	0.154	0.154	0.1562	0.178	0.1802	RANDOM	13.862

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]
0.43			0.66		-1.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.315
r_dihedral_angle_4_deg	13.302
r_dihedral_angle_3_deg	12.206
r_dihedral_angle_1_deg	5.758
r_scangle_it	1.603
r_angle_refined_deg	1.119
r_scbond_it	1.019
r_mcangle_it	0.636
r_mcbond_it	0.413
r_nbtor_refined	0.299
r_nbd_refined	0.187
r_symmetry_vdw_refined	0.145
r_symmetry_hbond_refined	0.118
r_xyhbond_nbd_refined	0.105
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16817
Nucleic Acid Atoms
Solvent Atoms	1807
Heterogen Atoms	172

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
REFMAC	phasing