5L50 | pdb_00005l50

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	6.5	298	200 mM MES/imidazol (pH 6.5) containing 100 mM NaCl, 30 % glycerol and 10 % PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.356	α = 90
b = 125.988	β = 90
c = 130.781	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	1.643	48.989	98.6	0.064	14.3	4.4		90521

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	1.643	1.651	95.1		0.669	1.9	4.2

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	1.643	48.989	88417	2100	98.57	0.1758	0.1753	0.1866	0.1956	0.2064	RANDOM	29.463

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		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.088
r_dihedral_angle_4_deg	20.557
r_dihedral_angle_3_deg	12.605
r_dihedral_angle_1_deg	5.894
r_angle_other_deg	3.561
r_angle_refined_deg	1.595
r_mcangle_it	1.417
r_mcbond_it	0.862
r_mcbond_other	0.857
r_chiral_restr	0.098
r_gen_planes_other	0.016
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3848
Nucleic Acid Atoms
Solvent Atoms	262
Heterogen Atoms	72

Software

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