2XD4 | pdb_00002xd4

Nucleotide-bound Structures of Bacillus subtilis Glycinamide Ribonucleotide Synthetase

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		30% PEG 4000, 0.1 M TRIS-HCL PH 8.5, 4.2 MM MGCL2, 1.8 MM ATP

Crystal Properties
Matthews coefficient	Solvent content
2.2	43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.99	α = 90
b = 84.41	β = 90
c = 85.72	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	IMAGE PLATE	RIGAKU RAXIS-IIC		1998-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200

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	2.65	38.21	93.4	0.1	22.6	4		11710			47.7

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	2.65	2.74	66.4		0.22

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 (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 2XCL	2.65	38.22	11710	11710	562	93.4	0.207	0.204	0.2	0.27	0.26	RANDOM	42.1

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]
-11.43			20.4		-8.97

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.9
c_scangle_it	2.88
c_mcangle_it	2.23
c_scbond_it	1.93
c_mcbond_it	1.3
c_angle_deg	0.9
c_improper_angle_d	0.65
c_bond_d	0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3164
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	30

Software

Software
Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing