Experiment: 1BDW

GRAMICIDIN D FROM BACILLUS BREVIS (ACTIVE FORM)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AV2	PDB ENTRY 1AV2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		2		CRYSTALLIZED BY BATCH METHODS FROM A 30 MG/ML SOLUTION OF GRAMICIDIN D IN GLACIAL ACETIC ACID, PH 2.0, BATCH METHOD

Crystal Properties
Matthews coefficient	Solvent content
1.65	25.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 20.584	α = 90
b = 27.905	β = 90
c = 52.04	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	295	IMAGE PLATE	RIGAKU RAXIS II	COLLIMATOR	1998-01-02	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH2R

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	1.7	100	95	0.05	0.05	28	3.4		11715		-3

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	1.7	1.76	58.8		0.125	0.125	3.5	1

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R	PDB ENTRY 1AV2	1.7	100	3416	159	95	0.18	0.168		0.1869	0.243	0.195	5% OF REFLECTIONS IN THIN RESOLUTION SHELLS.

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
7	292	316

RMS Deviations
Key	Refinement Restraint Deviation
s_from_restr_planes	0.237
s_non_zero_chiral_vol	0.054
s_zero_chiral_vol	0.045
s_similar_adp_cmpnt	0.043
s_angle_d	0.024
s_bond_d	0.007
s_similar_dist
s_anti_bump_dis_restr
s_rigid_bond_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	272
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms	20

Software

Software
Software Name	Purpose
AMoRE	phasing
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling