4PVQ

Crystal structure of sulfate-bound human l-asparaginase protein

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4GDT	pdb entry 4GDT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.27	293	0.2 M AMMONIUM IODIDE, 2.2 M AMMONIUM SULFATE, PH 5.27, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.22	α = 90
b = 59.22	β = 90
c = 298.5	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	IMAGE PLATE	RIGAKU RAXIS IV++	MIRRORS	2012-01-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	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	2.13	30	79.4	0.067	12.8		26285	26285

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	2.13	2.25	53.5		0.325	2.89	2.06

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 4GDT	2.13	30	24437	24437	1333	77.8	0.169	0.166	0.222	RANDOM	27.2

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			-0.18		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.177
r_dihedral_angle_3_deg	17.438
r_dihedral_angle_4_deg	14.413
r_dihedral_angle_1_deg	6.19
r_scangle_it	2.033
r_scbond_it	1.584
r_angle_refined_deg	1.298
r_mcangle_it	0.874
r_mcbond_it	0.488
r_chiral_restr	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4257
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	71

Software

Software
Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling