3CLM | pdb_00003clm

Crystal structure of transaldolase (YP_208650.1) from Neisseria gonorrhoeae FA 1090 at 1.14 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	NANODROP, 0.20M (NH4)2SO4, 20.0% PEG 3350, No Buffer pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2	VAPOR DIFFUSION, SITTING DROP	6.5	277	NANODROP, 0.16M Ca(OAc)2, 20.0% Glycerol, 14.4% PEG 8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.14	α = 90
b = 83.03	β = 90
c = 89.79	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-11-19	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2007-10-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97916	SSRL	BL11-1
2	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97953, 0.91840, 0.97939	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.14	29.579	90.4	0.043	10.68			107548		-3	6.167

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	1.14	1.18	44		0.326	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD, MOLECULAR REPLACEMENT	FREE R	1.14	29.579	107466	107466	5430	94	0.131	0.13	0.13	0.14	0.161	0.16	RANDOM	10.882

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]

RMS Deviations
Key	Refinement Restraint Deviation
s_zero_chiral_vol	0.072
s_non_zero_chiral_vol	0.069
s_similar_adp_cmpnt	0.047
s_approx_iso_adps	0.033
s_angle_d	0.029
s_from_restr_planes	0.027
s_anti_bump_dis_restr	0.019
s_bond_d	0.012
s_rigid_bond_adp_cmpnt	0.001
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2638
Nucleic Acid Atoms
Solvent Atoms	437
Heterogen Atoms	50

Software

Software
Software Name	Purpose
SHELXL-97	refinement
PHENIX	refinement
SHELX	phasing
SHELX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing
PHASER	phasing
MolProbity	model building

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.