3G59 | pdb_00003g59

Crystal Structure of Candida glabrata FMN Adenylyltransferase in complex with ATP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FWK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.4	289	0.1 M Sodium acetate, pH 4.4, 6% (w/v) PEG 4000, Temperature 289K, vapor diffusion, hanging drop

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.793	α = 90
b = 79.793	β = 90
c = 77.941	γ = 120

Symmetry
Space Group	P 32 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	113	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS	2007-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.87	50	99.9	0.078	21.984	5.2	24161	24161			21.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.87	1.94	99.6		0.549	2.456	4.5	2377

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	3FWK	1.87	50	24132	24132	1232	99.95	0.17661	0.177	0.174	0.17	0.222	0.22	RANDOM	20.596

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]
0.18	0.09		0.18		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.178
r_dihedral_angle_4_deg	15.262
r_dihedral_angle_3_deg	13.129
r_dihedral_angle_1_deg	4.581
r_scangle_it	3.406
r_scbond_it	2.294
r_angle_refined_deg	1.536
r_mcangle_it	1.501
r_mcbond_it	0.998
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.178
r_dihedral_angle_4_deg	15.262
r_dihedral_angle_3_deg	13.129
r_dihedral_angle_1_deg	4.581
r_scangle_it	3.406
r_scbond_it	2.294
r_angle_refined_deg	1.536
r_mcangle_it	1.501
r_mcbond_it	0.998
r_nbtor_refined	0.306
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.173
r_xyhbond_nbd_refined	0.122
r_chiral_restr	0.104
r_symmetry_hbond_refined	0.102
r_bond_refined_d	0.015
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2397
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms	44

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.