4PVP

Crystal structure of malonate-bound human L-asparaginase protein

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	2.2M SODIUM MALONATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.459	α = 90
b = 59.459	β = 90
c = 298.9	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	2011-11-11	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	1.85	30	94.7	0.047	18.4		48285	48285

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	1.85	1.96	69.5		0.249	2.58	1.9

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 2ZAK	1.85	29.73	45342	45342	2406	93.6	0.163	0.161	0.204	RANDOM	23.09

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]
-3.91			-3.91		7.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.905
r_dihedral_angle_3_deg	15.418
r_dihedral_angle_4_deg	13.64
r_dihedral_angle_1_deg	5.956
r_scangle_it	1.906
r_scbond_it	1.255
r_angle_refined_deg	1.21
r_mcangle_it	0.858
r_mcbond_it	0.488
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4309
Nucleic Acid Atoms
Solvent Atoms	251
Heterogen Atoms	9

Software

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