1YHT | pdb_00001yht

Crystal structure analysis of Dispersin B

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	PEG 10000, ammonium acetate, BisTris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2	38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.023	α = 90
b = 86.129	β = 90
c = 185.774	γ = 90

Symmetry
Space Group	C 2 2 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	ADSC QUANTUM 315		2004-06-01	M	SINGLE WAVELENGTH
2	1	x-ray		M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837, 0.979	SSRL	BL9-2

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	2	23.76	99.1	0.071	15.6	4.1	22562	21412	2	2

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	2	2.1	99.9		0.193	7.1	4

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	THROUGHOUT	2	23.76	22582	21412	1157	99.21	0.15421	0.15421	0.15116	0.16	0.21087	0.23	RANDOM	12.755

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
r_dihedral_angle_2_deg	38.845
r_dihedral_angle_4_deg	19.464
r_dihedral_angle_3_deg	15.291
r_dihedral_angle_1_deg	6.421
r_scangle_it	3.635
r_scbond_it	2.744
r_angle_refined_deg	1.623
r_mcbond_it	1.585
r_mcangle_it	1.555
r_angle_other_deg	0.904
r_symmetry_vdw_other	0.269
r_mcbond_other	0.244
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.217
r_nbd_other	0.193
r_nbtor_refined	0.183
r_symmetry_hbond_refined	0.166
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.107
r_nbtor_other	0.089
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2761
Nucleic Acid Atoms
Solvent Atoms	243
Heterogen Atoms	16

Software

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