2JFB

3D Structure of Lumazine Synthase from Candida albicans

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		pH 7.00

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.648	α = 90
b = 128.648	β = 90
c = 284.965	γ = 120

Symmetry
Space Group	P 31 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	100	IMAGE PLATE	MARRESEACH	MIRRORS	2005-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B		EMBL/DESY, HAMBURG	BW7B

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	2.5	15	99.8	0.08	9	4.1		94547		1	46.2

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	2.5	2.55	99.9		0.49	1.95	4.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1EJB	2.5	15	89819	4728	99.8	0.213	0.21	0.26	RANDOM	35.87

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]
-0.59	-0.29		-0.59		0.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.452
r_dihedral_angle_3_deg	14.224
r_dihedral_angle_4_deg	13.071
r_dihedral_angle_1_deg	4.172
r_angle_refined_deg	0.886
r_scangle_it	0.611
r_scbond_it	0.363
r_nbtor_refined	0.299
r_mcangle_it	0.252
r_nbd_refined	0.164
r_mcbond_it	0.142
r_symmetry_vdw_refined	0.141
r_xyhbond_nbd_refined	0.091
r_symmetry_hbond_refined	0.078
r_chiral_restr	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17904
Nucleic Acid Atoms
Solvent Atoms	751
Heterogen Atoms	99

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing