3KYU

X-ray crystal structure determination of fully perdeuterated rubredoxin at 100K

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop			3.8 M sodium/potassium phosphate, hanging drop

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.889	α = 90
b = 34.632	β = 90
c = 43.255	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	100	CCD	MAR225		2008-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	27.04					21196

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1BRF	1.1	27.04	20120	1076	99.61	0.10736	0.10645	0.12485	RANDOM	5.227

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]
-0.13			0.01		0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.558
r_dihedral_angle_3_deg	10.375
r_sphericity_free	8.161
r_dihedral_angle_1_deg	6.021
r_scangle_it	3.504
r_sphericity_bonded	3.465
r_scbond_it	2.5
r_mcangle_it	2.296
r_mcbond_it	2.032
r_angle_refined_deg	1.612
r_rigid_bond_restr	1.517
r_mcbond_other	1.097
r_angle_other_deg	0.911
r_nbd_refined	0.251
r_symmetry_vdw_other	0.19
r_nbtor_refined	0.188
r_nbd_other	0.183
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.125
r_symmetry_vdw_refined	0.118
r_chiral_restr	0.104
r_nbtor_other	0.09
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	421
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
ELVES	data reduction
ELVES	data scaling