3UMJ | pdb_00003umj

Crystal Structure of D311E Lipase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DSN	PDB ENTRY 2DSN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293.15	0.1M MES, 0.1M Sodium phosphate, 0.1M Potassium phosphate, 1.5M NaCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.323	α = 90
b = 81.162	β = 96.49
c = 100.14	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	Bruker Platinum 135		2010-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.540

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.1	37.57	96.9	0.0833	0.092		2.93		88705	5	4.9

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	2.1	2.2	91.4		0.1946	4.01	2.15

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2DSN	2.1	33.17	88705	50139	2677	96.78	0.15806	0.15518	0.1569	0.21163	0.2139	RANDOM	12.722

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]
		-0.01	0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.822
r_dihedral_angle_4_deg	19.483
r_dihedral_angle_3_deg	14.681
r_dihedral_angle_1_deg	6.43
r_scangle_it	4.822
r_scbond_it	3.108
r_mcangle_it	1.817
r_angle_refined_deg	1.786
r_mcbond_it	1.064
r_chiral_restr	0.128
r_bond_refined_d	0.022
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6102
Nucleic Acid Atoms
Solvent Atoms	622
Heterogen Atoms	26

Software

Software
Software Name	Purpose
PROTEUM PLUS	data collection
XPREP	data reduction
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling