5L4Z | pdb_00005l4z

Crystal structure of enzyme in purine metabolism

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J2C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	100 mM MOPS/HEPES-Na containing 100 mM NaCl, 15 % glycerol and 10 % PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.323	α = 90
b = 126.503	β = 90
c = 130.515	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2015-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918409	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.839	48.305	99.4	0.055	18.5	3.7		65417			35.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.839	1.849	99.1		0.71	2	3.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2J2C	1.84	45.42	63308	2101	99.41	0.1777	0.1768	0.1861	0.2049	0.21	RANDOM	38.287

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]
-0.01			0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.724
r_dihedral_angle_4_deg	17.57
r_dihedral_angle_3_deg	13.239
r_dihedral_angle_1_deg	6.277
r_angle_other_deg	3.562
r_mcangle_it	1.601
r_angle_refined_deg	1.561
r_mcbond_it	1.007
r_mcbond_other	0.995
r_chiral_restr	0.097
r_gen_planes_other	0.014
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3834
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	78

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building