4WHR | pdb_00004whr

Anhydride reaction intermediate trapped in Protocatechuate 3,4-dioxygenase (pseudomonas putida) at pH 8.5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3T63

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	295	1.2 M Ammonium Sulfate, 2.5 mM 2-mercaptoethanol, 100 mM Tris-HCl pH 8.5; 2:1 ratio of well sol. to 40 mg/ml protein solution in drop

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.437	α = 90
b = 140.644	β = 90
c = 168.291	γ = 90

Symmetry
Space Group	I 2 2 2

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	ADSC QUANTUM 315r		2014-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.58	50	91.4	0.142	0.162	0.076	12.2	4		188155

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.58	1.61	93.7		0.351	0.454	0.283	0.794		2.1	9578

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	3T63	1.58	31.47	188155	9462	91.33	0.1506	0.1484	0.15	0.1918	0.19	RANDOM	24.54

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]
-0.38			0.89		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.008
r_sphericity_free	22.307
r_dihedral_angle_4_deg	15.195
r_dihedral_angle_3_deg	12.91
r_sphericity_bonded	8.092
r_dihedral_angle_1_deg	6.554
r_rigid_bond_restr	4.098
r_angle_refined_deg	1.465
r_angle_other_deg	0.798
r_chiral_restr	0.118

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.008
r_sphericity_free	22.307
r_dihedral_angle_4_deg	15.195
r_dihedral_angle_3_deg	12.91
r_sphericity_bonded	8.092
r_dihedral_angle_1_deg	6.554
r_rigid_bond_restr	4.098
r_angle_refined_deg	1.465
r_angle_other_deg	0.798
r_chiral_restr	0.118
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10355
Nucleic Acid Atoms
Solvent Atoms	949
Heterogen Atoms	164

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
PDB_EXTRACT	data extraction
HKL-3000	data scaling
DENZO	data reduction
SCALEPACK	data scaling

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.