3RL4 | pdb_00003rl4

Rat metallophosphodiesterase MPPED2 G252H Mutant

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.2	293	MnCl2, PEG 3350, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.06	α = 90
b = 69.385	β = 102.96
c = 47.234	γ = 90

Symmetry
Space Group	C 1 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	MAR CCD 165 mm	monochromators, mirrors	2009-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R	0.99996	ELETTRA	5.2R

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	1.29	50	97.1	0.106	12.4	4	77182	74944		-3	13.88

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	1.29	1.32	89.7		0.378		3.5	4565

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.29	19.68	77099	74916	7557	97.17	0.1675	0.165	0.18	0.1905	0.19	RANDOM	20.2378

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]
1.34		-0.2	0.19		-1.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.622
r_dihedral_angle_4_deg	13.559
r_dihedral_angle_3_deg	11.322
r_dihedral_angle_1_deg	6.383
r_sphericity_free	4.084
r_scangle_it	2.844
r_sphericity_bonded	2.836
r_scbond_it	2.51
r_rigid_bond_restr	2.113
r_mcangle_it	1.683
r_angle_refined_deg	1.295
r_mcbond_it	1.092
r_nbtor_refined	0.316
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.166
r_xyhbond_nbd_refined	0.095
r_chiral_restr	0.091
r_symmetry_hbond_refined	0.044
r_bond_refined_d	0.009
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2213
Nucleic Acid Atoms
Solvent Atoms	293
Heterogen Atoms	37

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction