5IZR | pdb_00005izr

Human GIVD cytosolic phospholipase A2 in complex with Methyl gamma-Linolenyl Fluorophosphonate inhibitor and Terbium Chloride

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	100 mM MES (pH 6.0-6.2), 10-14% (v/v) PEG20K and 50 mM sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.824	α = 90
b = 112.667	β = 90.03
c = 159.2	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315r		2015-01-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.650	ALS	5.0.2

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	3.25	159.2	99.6	0.162	9.9	7.5		56076

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.25	3.34	99.2		2.1	7.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	3.25	159.2	53210	2849	99.51	0.23174	0.22988	0.2341	0.26654	0.2642	RANDOM	85.699

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]
-2.56		-0.1	10.17		-7.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.241
r_dihedral_angle_3_deg	18.843
r_dihedral_angle_4_deg	16.753
r_long_range_B_refined	11.221
r_long_range_B_other	11.221
r_mcangle_it	7.348
r_mcangle_other	7.348
r_scangle_other	7.344
r_dihedral_angle_1_deg	6.71
r_mcbond_it	4.438
r_mcbond_other	4.438
r_scbond_it	4.333
r_scbond_other	4.333
r_angle_refined_deg	1.291
r_angle_other_deg	0.882
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21254
Nucleic Acid Atoms
Solvent Atoms	12
Heterogen Atoms	103

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing