3RL5 | pdb_00003rl5

Rat metallophosphodiesterase MPPED2 H67R Mutant

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	293	Ammonium nitrate, PEG 3350, CaCl2, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.622	α = 90
b = 69.848	β = 103.52
c = 47.182	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	1.26	50	99.9	0.059	16.9	4.1	84002	83943		-3	11.242

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	1.26	1.29	99.2		0.251		3.9	5512

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	1.26	20.75	84002	83935	8430	99.92	0.1542	0.1519	0.16	0.1744	0.18	RANDOM	16.8614

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]
0.27		-0.39	-0.1		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.423
r_dihedral_angle_4_deg	14.253
r_dihedral_angle_3_deg	10.556
r_dihedral_angle_1_deg	6.279
r_sphericity_free	5.16
r_sphericity_bonded	4.09
r_scangle_it	3.475
r_scbond_it	3.124
r_rigid_bond_restr	2.939
r_mcangle_it	2.045
r_mcbond_it	1.389
r_angle_refined_deg	1.323
r_nbtor_refined	0.318
r_symmetry_vdw_refined	0.301
r_nbd_refined	0.199
r_symmetry_metal_ion_refined	0.126
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.094
r_metal_ion_refined	0.092
r_symmetry_hbond_refined	0.061
r_bond_refined_d	0.011
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2250
Nucleic Acid Atoms
Solvent Atoms	285
Heterogen Atoms	10

Software

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