3G9X | pdb_00003g9x

Structure of haloalkane dehalogenase DhaA14 mutant I135F from Rhodococcus rhodochrous

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BN6	PDB ENTRY 1BN6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		9	277	[protein]=7-10 mg/ml in 50mM Tris-HCl buffer pH 7.5; [Precipitant]=25% PEG 4000, 8% 2-propanol in 100mM sodium acetate., VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.14	40.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.73	α = 115.5
b = 44.44	β = 97.87
c = 46.63	γ = 109.52

Symmetry
Space Group	P 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		2007-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11		EMBL/DESY, HAMBURG	X11

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	0.95	30	94.2	0.059	0.059	26.4	5.8		163495			7.9

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	0.95	0.97	90.6		0.418	0.418	4.4	4

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 (All)	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	FREE R	PDB ENTRY 1BN6	0.95	10	163371	163371	8179	94.2	0.1149	0.1149	0.1149	0.12	0.1374	0.13	RANDOM	8.763

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]
0.14	0.14	0.41	0.03	0.3	0.3

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
64	2132.7	2881.55

RMS Deviations
Key	Refinement Restraint Deviation
s_zero_chiral_vol	0.104
s_non_zero_chiral_vol	0.1
s_anti_bump_dis_restr	0.036
s_similar_adp_cmpnt	0.033
s_angle_d	0.031
s_from_restr_planes	0.0283
s_bond_d	0.015
s_rigid_bond_adp_cmpnt	0.005
s_similar_dist
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2372
Nucleic Acid Atoms
Solvent Atoms	520
Heterogen Atoms	9

Software

Software
Software Name	Purpose
SHELXL-97	refinement
MOLREP	phasing
REFMAC	refinement
Coot	model building
MolProbity	model building
DENZO	data reduction
SCALEPACK	data scaling
HKL-2000	data collection

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.