3EZW | pdb_00003ezw

Crystal Structure of a Hyperactive Escherichia coli Glycerol Kinase Mutant Gly230 --> Asp Obtained Using Microfluidic Crystallization Devices

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GLF	pdb entry 1GLF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microfluidic free interface diffusion	8.5	298	20% PEG 1500, 0.3 M MAGNESIUM CHLORIDE, 0.1 M TRIS-HCL, pH 8.5, microfluidic free interface diffusion, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.116	α = 90
b = 114.26	β = 91.15
c = 212.624	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 4		2006-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-3	0.97	SSRL	BL11-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	50	84	0.059	36.8	5.9		250186

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05	73.2		0.225	6.6	3.4

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	pdb entry 1GLF	2	20	246407	5032	84.05	0.1679	0.16673	0.17	0.22478	0.23	RANDOM	24.437

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]
-2.23		0.59	0.97		1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.247
r_dihedral_angle_4_deg	19.763
r_dihedral_angle_3_deg	15.477
r_dihedral_angle_1_deg	7.024
r_scangle_it	4.689
r_scbond_it	2.989
r_angle_refined_deg	1.893
r_mcangle_it	1.872
r_angle_other_deg	1.673
r_mcbond_it	1.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.247
r_dihedral_angle_4_deg	19.763
r_dihedral_angle_3_deg	15.477
r_dihedral_angle_1_deg	7.024
r_scangle_it	4.689
r_scbond_it	2.989
r_angle_refined_deg	1.893
r_mcangle_it	1.872
r_angle_other_deg	1.673
r_mcbond_it	1.107
r_mcbond_other	0.338
r_chiral_restr	0.116
r_bond_refined_d	0.024
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	31113
Nucleic Acid Atoms
Solvent Atoms	1526
Heterogen Atoms	133

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

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.