Experiment: 4LQR

Structure of CBM32-3 from a family 31 glycoside hydrolase from Clostridium perfringens

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J1A	PDB ENTRY 2J1A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	20% PEG 10000, 100mM HEPES 50mM NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.766	α = 90
b = 52.562	β = 90
c = 70.169	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	93.15	CCD	ADSC QUANTUM 210		2009-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.98	NSLS	X6A

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	1.58	50	98.9	0.042		5.4		20155

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	1.58	1.64	91		0.084		7.6	1833

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2J1A	1.58	33.96	20155	1024	99.83	0.1626	0.1609	0.194	0.2181	RANDOM	9.8579

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]
-0.42			-0.11		0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.04
r_dihedral_angle_4_deg	16.052
r_dihedral_angle_3_deg	12.037
r_dihedral_angle_1_deg	7.194
r_angle_refined_deg	2.248
r_chiral_restr	0.178
r_bond_refined_d	0.024
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1238
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing