2IGD | pdb_00002igd

ANISOTROPIC STRUCTURE OF PROTEIN G IGG-BINDING DOMAIN III AT 1.1 ANGSTROM RESOLUTION

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8		CRYSTALS WERE GROWN BY HANGING DROP VAPOUR DIFFUSION FROM 24-26% PEG 4000, 10MM SODIUM ACETATE AT PH 4.8 AND 0.01% SODIUM AZIDE. CELL PARAMETERS ARE NOT THOSE DETERMINED EXPERIMENTALLY. THEY WERE ADJUSTED ON THE BASIS OF THE ENGH & HUBER DICTIONARY AT THE END OF REFINEMENT. THE EXPERIMENTAL ESTIMATES WERE KNOWN TO HAVE POTENTIAL ERRORS DUE TO INACCURACIES IN THE CRYSTAL-TO-DETECTOR AND WAVELENGTH CALIBRATION., vapor diffusion - hanging drop

Crystal Properties
Matthews coefficient	Solvent content
2.23	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.05	α = 90
b = 40.5	β = 90
c = 42.37	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	300	IMAGE PLATE	MARRESEARCH	TOROIDAL MIRROR	1992-04-05	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X31		EMBL/DESY, HAMBURG	X31

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	1.1	10.1	97.9	0.037	0.037	39	4.8		24145

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	1.1	1.12	98.1		0.104	0.104	12	3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	INITIAL MODEL WAS PREVIOUSLY OBTAINED STRUCTURE	FREE R-VALUE	PDB ENTRY 1IGD	1.1	10	24145	1233	97.9	0.097	0.097		0.11	0.125	5%, RANDOMLY

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
9	409.9	571.7

RMS Deviations
Key	Refinement Restraint Deviation
s_from_restr_planes	0.371
s_non_zero_chiral_vol	0.139
s_approx_iso_adps	0.117
s_zero_chiral_vol	0.115
s_similar_adp_cmpnt	0.042
s_angle_d	0.028
s_bond_d	0.02
s_rigid_bond_adp_cmpnt	0.006
s_similar_dist
s_anti_bump_dis_restr

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	468
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms

Software

Software
Software Name	Purpose
SHELXL-96	model building
SHELXL-96	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELXL-96	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.