2PYS | pdb_00002pys

Crystal Structure of a Five Site Mutated Cyanovirin-N with a Mannose Dimer Bound at 1.8 A Resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LOM	pdb entry 1LOM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	30% PEG 8000, 100 MM MGSO4, 2 MM MAN2, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.226	α = 90
b = 38.281	β = 99.69
c = 55.794	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS	2005-11-09	M	SINGLE WAVELENGTH

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

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	1.8	55.22	87.7	0.094	8.13	1.9		19361		4

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)
	1.8	1.85	82.33		0.244	2.92	1.4

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1LOM	1.8	9.99	17236	924	94.5	0.171	0.169	0.19	0.215	0.18	RANDOM	22.49

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]
0.05		-0.04	0.08		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.064
r_dihedral_angle_4_deg	15.907
r_dihedral_angle_3_deg	13.36
r_dihedral_angle_1_deg	6.977
r_sphericity_free	6.754
r_scangle_it	4.11
r_scbond_it	3.53
r_sphericity_bonded	2.364
r_rigid_bond_restr	2.254
r_mcangle_it	1.83
r_mcbond_it	1.753
r_angle_refined_deg	1.733
r_angle_other_deg	1.389
r_mcbond_other	0.449
r_xyhbond_nbd_refined	0.284
r_nbd_refined	0.218
r_chiral_restr	0.212
r_symmetry_vdw_other	0.21
r_nbd_other	0.209
r_symmetry_vdw_refined	0.176
r_nbtor_refined	0.168
r_symmetry_hbond_refined	0.107
r_nbtor_other	0.092
r_bond_other_d	0.029
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1539
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms	46

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling