1VKQ | pdb_00001vkq

A re-determination of the structure of the triple mutant (K53,56,120M) of phospholipase A2 at 1.6A resolution using sulphur-SAS at 1.54A wavelength

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	vapor diffusion method	7.2	293	50 mM Tris Buffer, 70% MPD reservoir,17-20Mg/ml prot,5 mM CaCl2 and 60% MPD in the droplet, pH 7.2, vapor diffusion method, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.05	α = 90
b = 46.05	β = 90
c = 101.58	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	CCD	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9A		NSLS	X9A

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	1.6	19.96		0.059	50.1	12.1		17048

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)
	1.6	1.66			0.284			3188

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SULPHUR-SAS	THROUGHOUT	1.6	19.96	17048	16184	860	99.66	0.17893	0.17703	0.18	0.21658	0.21	RANDOM	24.462

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]
-0.02	-0.01		-0.02		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.62
r_scangle_it	4.071
r_scbond_it	2.569
r_mcangle_it	1.671
r_angle_refined_deg	1.536
r_mcbond_it	0.88
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.173
r_symmetry_hbond_refined	0.123
r_chiral_restr	0.097
r_metal_ion_refined	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	954
Nucleic Acid Atoms
Solvent Atoms	189
Heterogen Atoms	2

Software

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