4R9K | pdb_00004r9k

Structure of thermostable eightfold mutant of limonene epoxide hydrolase from Rhodococcus erythropolis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NWW	PDB ENTRY 1NWW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.4	294	1.44 M tri-sodium citrate, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.049	α = 90
b = 88.049	β = 90
c = 110.241	γ = 120

Symmetry
Space Group	P 32 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	77	PIXEL	DECTRIS PILATUS 6M		2012-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.97625	ESRF	ID29

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	1.45	76.253	99.9	0.073	0.024	18	9.9		87794	2.9	2.9	13.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.53	99.6		0.902	0.296	2.9	10	12648

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 1NWW	1.5	44	2	75382	75382	4008	99.89	0.14261	0.14143	0.15	0.16476	0.17	RANDOM	18.991

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]
0.36	0.18		0.36		-1.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.83
r_dihedral_angle_4_deg	19.587
r_dihedral_angle_3_deg	12.727
r_dihedral_angle_1_deg	6.612
r_long_range_B_refined	5.979
r_long_range_B_other	5.979
r_scangle_other	4.942
r_scbond_it	3.344
r_scbond_other	3.343
r_mcangle_other	2.481
r_mcangle_it	2.468
r_angle_refined_deg	2.275
r_mcbond_it	1.748
r_mcbond_other	1.729
r_angle_other_deg	0.976
r_chiral_restr	0.16
r_bond_refined_d	0.024
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3606
Nucleic Acid Atoms
Solvent Atoms	362
Heterogen Atoms	57

Software

Software
Software Name	Purpose
tvx	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling